Variant report

Variant	rs1878904
Chromosome Location	chr2:86114252-86114253
allele	G/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	NFIC	chr2:86113520-86114302	SK-N-SH	brain:	n/a	n/a
2	MXI1	chr2:86112995-86117346	IMR90	lung:	n/a	n/a
3	MAX	chr2:86113503-86115849	A549	lung:	n/a	n/a
4	FOSL2	chr2:86113578-86114259	SK-N-SH	brain:	n/a	chr2:86113776-86113785
5	BCL3	chr2:86113677-86114651	A549	lung:	n/a	n/a
6	MAX	chr2:86113538-86114253	SK-N-SH	brain:	n/a	n/a
7	EP300	chr2:86113468-86114298	SK-N-SH	brain:	n/a	n/a
8	MAX	chr2:86113505-86114263	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr2:86113563-86114272	SK-N-SH	brain:	n/a	n/a
10	WRNIP1	chr2:86113446-86115563	GM12878	blood:	n/a	n/a
11	CTCF	chr2:86113541-86117024	A549	lung:	n/a	chr2:86116282-86116295 chr2:86114925-86114943 chr2:86114928-86114941 chr2:86114927-86114948 chr2:86116280-86116298 chr2:86114314-86114322 chr2:86114930-86114940
12	MAX	chr2:86112960-86118329	A549	lung:	n/a	chr2:86116152-86116161 chr2:86115924-86115934
13	TCF12	chr2:86113441-86114364	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr2:86113629-86115662	A549	lung:	n/a	chr2:86115492-86115502
15	MXI1	chr2:86113402-86114290	SK-N-SH	brain:	n/a	n/a
16	PBX3	chr2:86113543-86114270	SK-N-SH	brain:	n/a	n/a
17	ZNF263	chr2:86113413-86115552	HEK293-T-REx	kidney:	n/a	n/a
18	MXI1	chr2:86114250-86115503	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86112427..86114541-chr8:128877788..128879604,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232504	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10496320	0.84[JPT][hapmap]
rs11127006	0.84[JPT][hapmap]
rs1135603	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12614498	0.82[CHB][hapmap]
rs12622987	0.84[JPT][hapmap]
rs13008291	0.90[ASN][1000 genomes]
rs13014421	0.84[JPT][hapmap]
rs1401384	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1518983	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1518991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17026675	0.83[JPT][hapmap]
rs17026750	0.91[CEU][hapmap]
rs1878898	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];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1878899	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577770	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577771	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577772	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577774	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577775	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577777	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577778	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577779	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577780	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577786	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2679710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2679712	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679714	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2679715	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2679716	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2679717	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679718	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679719	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2679720	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2679721	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2679722	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs2679725	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28364794	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2918014	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2918015	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2918016	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2945823	0.86[EUR][1000 genomes]
rs2945825	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2945826	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35153287	0.85[EUR][1000 genomes]
rs3810821	0.84[JPT][hapmap]
rs4832016	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4832210	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4832216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832217	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];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4832218	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62150576	0.91[ASN][1000 genomes]
rs6547636	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap]
rs6720161	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap]
rs6734115	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6735629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747179	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747294	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6750686	0.87[CEU][hapmap];0.82[YRI][hapmap]
rs7572209	0.84[JPT][hapmap]
rs764471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs954176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1878904	C2orf51	cis	cerebellum	SCAN
rs1878904	ST3GAL5	cis	cerebellum	SCAN
rs1878904	PTCD3	cis	cerebellum	SCAN
rs1878904	IMMT	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86102800-86115200	Weak transcription	Small Intestine	intestine
2	chr2:86106400-86115200	Weak transcription	Gastric	stomach
3	chr2:86111000-86114600	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:86112000-86114600	Enhancers	Primary hematopoietic stem cells	blood
5	chr2:86112000-86114600	Enhancers	Stomach Mucosa	stomach
6	chr2:86112200-86114400	Genic enhancers	Primary B cells from cord blood	blood
7	chr2:86112200-86114600	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:86112200-86114600	Enhancers	Liver	Liver
9	chr2:86112200-86114600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:86112400-86114400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:86112400-86114600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:86112400-86115000	Enhancers	Spleen	Spleen
13	chr2:86113000-86114400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:86113000-86115000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr2:86113000-86115000	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr2:86113000-86115400	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr2:86113000-86115600	Flanking Active TSS	Dnd41	blood
18	chr2:86113200-86114600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr2:86113200-86114600	Active TSS	Duodenum Mucosa	Duodenum
20	chr2:86113200-86114800	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr2:86113200-86115000	Flanking Active TSS	A549	lung
22	chr2:86113400-86114800	Enhancers	HUVEC	blood vessel
23	chr2:86113400-86115000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr2:86113400-86115600	Flanking Active TSS	HSMM	muscle
25	chr2:86113600-86114600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:86113600-86114600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:86113600-86114600	Flanking Active TSS	Thymus	Thymus
28	chr2:86113600-86114800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:86113600-86114800	Enhancers	Hela-S3	cervix
30	chr2:86113600-86115000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:86113600-86115000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:86113600-86115200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:86113600-86115600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:86113600-86115600	Flanking Active TSS	Fetal Thymus	thymus
35	chr2:86113600-86115600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr2:86113600-86115800	Flanking Active TSS	NH-A	brain
37	chr2:86113800-86114400	Enhancers	Fetal Kidney	kidney
38	chr2:86113800-86114400	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr2:86113800-86114600	Enhancers	Brain Germinal Matrix	brain
40	chr2:86113800-86114600	Enhancers	Fetal Stomach	stomach
41	chr2:86113800-86114600	Enhancers	Pancreas	Pancrea
42	chr2:86113800-86114800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
43	chr2:86113800-86114800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:86113800-86115000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
45	chr2:86113800-86115000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:86113800-86115000	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr2:86113800-86115000	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr2:86113800-86115200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:86113800-86115400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:86113800-86115400	Flanking Active TSS	Rectal Smooth Muscle	rectum

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