Variant report

Variant	rs1168974
Chromosome Location	chr2:96814928-96814929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr2:96814045-96814947	K562	blood:	n/a	chr2:96814391-96814399 chr2:96814388-96814396
2	ESRRA	chr2:96807401-96815327	GM12878	blood:	n/a	chr2:96814549-96814568 chr2:96812831-96812844 chr2:96814530-96814543 chr2:96808836-96808848 chr2:96812889-96812902
3	SMARCC1	chr2:96813402-96815037	Hela-S3	cervix:	n/a	chr2:96814390-96814399
4	CREB1	chr2:96814009-96814928	H1-hESC	embryonic stem cell:	n/a	n/a
5	ELF1	chr2:96814062-96814976	GM12878	blood:	n/a	n/a
6	MAZ	chr2:96814064-96814974	Hela-S3	cervix:	n/a	chr2:96814921-96814930 chr2:96814534-96814544
7	EP300	chr2:96811760-96815004	SK-N-SH	brain:	n/a	chr2:96813968-96813982 chr2:96812145-96812161 chr2:96812146-96812162
8	ZEB1	chr2:96814078-96814971	GM12878	blood:	n/a	chr2:96814545-96814554
9	WRNIP1	chr2:96814865-96814967	GM12878	blood:	n/a	n/a
10	MAX	chr2:96814064-96815020	Hela-S3	cervix:	n/a	chr2:96814921-96814930 chr2:96814534-96814544
11	EP300	chr2:96813277-96815068	GM12878	blood:	n/a	chr2:96813968-96813982
12	MAX	chr2:96814832-96815047	K562	blood:	n/a	chr2:96814921-96814930
13	MTA3	chr2:96806625-96815107	GM12878	blood:	n/a	n/a
14	CREB1	chr2:96813650-96815001	GM12878	blood:	n/a	n/a
15	KAP1	chr2:96812525-96814932	HEK293	kidney:	n/a	chr2:96814389-96814398
16	USF2	chr2:96814128-96815003	GM12878	blood:	n/a	n/a
17	JUND	chr2:96813935-96815078	SK-N-SH	brain:	n/a	chr2:96814391-96814399 chr2:96814388-96814396 chr2:96814389-96814400
18	HCFC1	chr2:96813650-96815162	Hela-S3	cervix:	n/a	n/a
19	SMARCB1	chr2:96814124-96815005	Hela-S3	cervix:	n/a	chr2:96814390-96814399
20	ELK1	chr2:96814237-96814932	Hela-S3	cervix:	n/a	n/a
21	JUND	chr2:96814106-96815011	GM12878	blood:	n/a	chr2:96814391-96814399 chr2:96814388-96814396 chr2:96814389-96814400

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96813186..96815760-chr2:96873244..96875582,3	MCF-7	breast:
2	chr2:96814366..96815909-chr2:96816931..96819654,2	K562	blood:

Variant related genes	Relation type
ENSG00000228873	TF binding region
DUSP2	TF binding region
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10183151	0.95[CEU][hapmap];0.80[YRI][hapmap];0.91[EUR][1000 genomes]
rs1030864	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11680950	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11687113	0.92[GIH][hapmap]
rs1168965	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168966	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs1168967	0.83[EUR][1000 genomes]
rs1168968	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168972	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168976	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11693248	0.83[EUR][1000 genomes]
rs13019188	0.80[CEU][hapmap]
rs1657502	0.82[CEU][hapmap];0.84[GIH][hapmap];0.80[EUR][1000 genomes]
rs1724121	0.85[EUR][1000 genomes]
rs1724125	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2140938	0.84[EUR][1000 genomes]
rs2229169	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301707	1.00[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs2312955	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2438978	0.80[YRI][hapmap]
rs2462774	0.87[YRI][hapmap]
rs2576437	0.84[EUR][1000 genomes]
rs2579519	0.81[GIH][hapmap]
rs2579549	0.85[EUR][1000 genomes]
rs2579550	0.86[EUR][1000 genomes]
rs2579552	0.87[EUR][1000 genomes]
rs2692893	0.84[ASW][hapmap];0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2692894	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2692934	0.86[EUR][1000 genomes]
rs2692936	0.86[EUR][1000 genomes]
rs2692937	0.87[EUR][1000 genomes]
rs2917662	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2969490	0.86[CEU][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs2969491	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3111873	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821051	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4144055	0.91[GIH][hapmap];0.88[YRI][hapmap]
rs4426564	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap]
rs4907299	0.90[CEU][hapmap];0.85[GIH][hapmap];0.90[EUR][1000 genomes]
rs58448550	0.83[EUR][1000 genomes]
rs6740563	0.89[YRI][hapmap]
rs749457	0.82[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs749459	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs7561198	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7604842	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs772175	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs772178	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap]
rs893173	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1004129	chr2:96738585-96825363	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
7	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
8	nsv874675	chr2:96741944-96825363	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv874676	chr2:96753149-96825363	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv1819594	chr2:96755038-96833480	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv1008495	chr2:96755070-96825363	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv1002392	chr2:96756289-96815149	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
14	nsv1004977	chr2:96757107-96819188	Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv1015000	chr2:96757107-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
17	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
18	nsv1007132	chr2:96767204-96829489	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1168974	MRPL30	cis	parietal	SCAN
rs1168974	GPAT2	cis	Muscle Skeletal	GTEx
rs1168974	ADRA2B	cis	Nerve Tibial	GTEx
rs1168974	FAHD2CP	cis	Muscle Skeletal	GTEx
rs1168974	MGAT4A	cis	parietal	SCAN
rs1168974	ADRA2B	cis	Thyroid	GTEx
rs1168974	GPAT2	cis	Adipose Subcutaneous	GTEx
rs1168974	SNRNP200	cis	cerebellum	SCAN
rs1168974	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs1168974	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs1168974	FAHD2CP	cis	lung	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96810000-96815000	Enhancers	Fetal Heart	heart
2	chr2:96810400-96815000	Enhancers	Fetal Lung	lung
3	chr2:96811200-96815000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:96811200-96815000	Enhancers	NH-A	brain
5	chr2:96811200-96815200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:96811400-96815000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:96811400-96815200	Flanking Active TSS	Hela-S3	cervix
8	chr2:96811600-96815000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:96811600-96815000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr2:96811600-96815000	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr2:96811600-96815000	Enhancers	Right Ventricle	heart
12	chr2:96811600-96815000	Enhancers	HMEC	breast
13	chr2:96811600-96815200	Enhancers	Fetal Stomach	stomach
14	chr2:96811800-96815000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:96811800-96815200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:96812200-96815000	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr2:96812200-96815200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:96812400-96815000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr2:96812400-96815000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr2:96812400-96815000	Flanking Active TSS	Thymus	Thymus
21	chr2:96812400-96815200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr2:96812400-96815200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:96812400-96815400	Enhancers	Primary B cells from cord blood	blood
24	chr2:96812600-96815000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr2:96812600-96815000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:96812600-96815000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:96812600-96815200	Enhancers	NHEK	skin
28	chr2:96812600-96815400	Enhancers	Primary hematopoietic stem cells	blood
29	chr2:96812800-96815400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr2:96813000-96815000	Enhancers	Fetal Intestine Large	intestine
31	chr2:96813000-96815000	Enhancers	Dnd41	blood
32	chr2:96813000-96815200	Enhancers	Primary T cells from cord blood	blood
33	chr2:96813000-96815400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:96813200-96815000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr2:96813400-96815000	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr2:96813600-96815000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:96813600-96815000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:96813600-96822000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:96813800-96815000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr2:96813800-96815000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr2:96813800-96815000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:96813800-96815000	Bivalent Enhancer	Fetal Intestine Small	intestine
43	chr2:96814000-96815000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr2:96814000-96815000	Enhancers	Placenta Amnion	Placenta Amnion
45	chr2:96814000-96815000	Enhancers	NHLF	lung
46	chr2:96814200-96815200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:96814200-96815400	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr2:96814400-96815000	Enhancers	Gastric	stomach
49	chr2:96814400-96815200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:96814400-96840000	Weak transcription	Right Atrium	heart

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