Variant report

Variant	rs7608621
Chromosome Location	chr2:97483783-97483784
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	POLR2A	chr2:97481096-97483863	GM12878	blood:	n/a	n/a
2	ZNF263	chr2:97481138-97486512	HEK293-T-REx	kidney:	n/a	chr2:97486292-97486301 chr2:97484433-97484454
3	ZMIZ1	chr2:97483656-97483925	K562	blood:	n/a	n/a
4	MAFK	chr2:97483753-97483953	HepG2	liver:	n/a	chr2:97483823-97483837 chr2:97483824-97483839 chr2:97483824-97483840 chr2:97483825-97483836 chr2:97483824-97483835 chr2:97483824-97483835
5	EP300	chr2:97483524-97483851	K562	blood:	n/a	n/a
6	TAL1	chr2:97483613-97483885	K562	blood:	n/a	n/a
7	MXI1	chr2:97480568-97483974	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr2:97480952-97484103	HepG2	liver:	n/a	n/a
9	TEAD4	chr2:97483499-97483966	K562	blood:	n/a	n/a
10	CUX1	chr2:97483688-97483861	K562	blood:	n/a	n/a
11	POLR2A	chr2:97483726-97484000	K562	blood:	n/a	n/a
12	GATA2	chr2:97483539-97483925	K562	blood:	n/a	chr2:97483766-97483773 chr2:97483766-97483775 chr2:97483739-97483749 chr2:97483741-97483748 chr2:97483736-97483752 chr2:97483765-97483775 chr2:97483739-97483748 chr2:97483738-97483750
13	USF2	chr2:97483666-97483804	K562	blood:	n/a	n/a
14	MAFK	chr2:97483697-97483957	K562	blood:	n/a	chr2:97483823-97483837 chr2:97483824-97483839 chr2:97483824-97483840 chr2:97483825-97483836 chr2:97483824-97483835 chr2:97483824-97483835
15	TBL1XR1	chr2:97483594-97483880	K562	blood:	n/a	n/a
16	RCOR1	chr2:97483605-97483909	K562	blood:	n/a	n/a
17	TEAD4	chr2:97483564-97483907	K562	blood:	n/a	n/a
18	MAFK	chr2:97483716-97483970	HepG2	liver:	n/a	chr2:97483823-97483837 chr2:97483824-97483839 chr2:97483824-97483840 chr2:97483825-97483836 chr2:97483824-97483835 chr2:97483824-97483835
19	MYC	chr2:97483601-97483918	K562	blood:	n/a	n/a
20	CTCF	chr2:97483754-97483832	Lung_OC	lung:	n/a	n/a
21	MAFF	chr2:97483647-97483895	HepG2	liver:	n/a	n/a
22	MAZ	chr2:97483697-97483876	K562	blood:	n/a	n/a
23	MAFF	chr2:97483639-97483873	K562	blood:	n/a	n/a
24	JUND	chr2:97483694-97483914	K562	blood:	n/a	chr2:97483830-97483840 chr2:97483830-97483840

No.	Distal block	Cell Line	Cell type
1	chr2:97302043..97304772-chr2:97480834..97485283,4	K562	blood:
2	chr2:97481636..97484312-chr2:97528160..97530681,3	MCF-7	breast:
3	chr2:97482890..97484803-chr2:97649558..97651545,2	MCF-7	breast:
4	chr2:97481648..97486150-chr2:97531417..97538119,10	MCF-7	breast:
5	chr2:97303859..97305572-chr2:97481972..97484956,2	K562	blood:
6	chr2:97480973..97483903-chr2:97621623..97628750,6	MCF-7	breast:
7	chr2:97483756..97486105-chr2:97524140..97526668,2	K562	blood:
8	chr2:97424794..97426969-chr2:97483336..97486103,2	MCF-7	breast:
9	chr2:97481193..97483827-chr2:97615548..97618256,2	MCF-7	breast:
10	chr2:97482077..97484941-chr2:97522185..97524472,2	MCF-7	breast:
11	chr2:97302401..97304754-chr2:97481583..97484330,2	MCF-7	breast:
12	chr2:97425678..97429518-chr2:97479689..97484495,7	MCF-7	breast:
13	chr2:97481330..97485256-chr2:97521136..97525640,5	K562	blood:
14	chr2:97483777..97486201-chr2:97534208..97536891,3	K562	blood:
15	chr2:97482548..97484049-chr5:176980916..176982734,2	MCF-7	breast:
16	chr2:97482924..97486110-chr2:97522270..97524804,3	MCF-7	breast:
17	chr2:97482549..97484070-chr5:176981046..176982847,2	MCF-7	breast:
18	chr2:97480844..97484629-chr2:97532869..97536982,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273265	TF binding region
ENSG00000168754	Chromatin interaction
ENSG00000213337	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000114982	Chromatin interaction
ENSG00000158158	Chromatin interaction
ENSG00000146067	Chromatin interaction
ENSG00000163126	Chromatin interaction
ENSG00000252845	Chromatin interaction
ENSG00000272459	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11897786	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12846	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320146	0.87[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1320149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419073	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs17119598	0.87[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs2276654	0.87[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs3731941	0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs55674661	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58147284	0.81[AMR][1000 genomes]
rs62152788	0.82[EUR][1000 genomes]
rs62152790	0.84[EUR][1000 genomes]
rs62152793	0.87[EUR][1000 genomes]
rs62152794	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62152795	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576986	0.87[CEU][hapmap]
rs6576987	0.87[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs6576989	1.00[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6753987	1.00[MEX][hapmap];0.82[TSI][hapmap]
rs7580942	1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7594727	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[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9948	0.87[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs9973492	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	esv3419974	chr2:97480425-97484723	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	esv3522461	chr2:97480625-97484323	Flanking Active TSS Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	esv3522462	chr2:97481225-97484298	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	esv3522464	chr2:97481225-97484298	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7608621	FAHD2CP	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97481000-97484000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr2:97481200-97484000	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr2:97482800-97483800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:97482800-97483800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:97482800-97483800	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr2:97482800-97483800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr2:97482800-97483800	Flanking Active TSS	Colonic Mucosa	Colon
8	chr2:97482800-97483800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr2:97482800-97483800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr2:97482800-97484000	Flanking Active TSS	Liver	Liver
11	chr2:97482800-97484000	Flanking Active TSS	Right Ventricle	heart
12	chr2:97482800-97484000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr2:97482800-97484400	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr2:97482800-97484600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr2:97482800-97485200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:97482800-97485400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:97483000-97483800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr2:97483000-97483800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr2:97483000-97483800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
20	chr2:97483000-97483800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:97483000-97483800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr2:97483000-97483800	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr2:97483000-97483800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:97483000-97483800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr2:97483000-97483800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:97483000-97483800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr2:97483000-97483800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr2:97483000-97483800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:97483000-97483800	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:97483000-97483800	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr2:97483000-97483800	Flanking Active TSS	Ovary	ovary
32	chr2:97483000-97483800	Flanking Active TSS	Thymus	Thymus
33	chr2:97483000-97483800	Flanking Active TSS	NHDF-Ad	bronchial
34	chr2:97483000-97484000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
35	chr2:97483000-97484000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:97483000-97484000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
37	chr2:97483000-97484000	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr2:97483000-97484000	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr2:97483000-97484000	Flanking Active TSS	Fetal Brain Female	brain
40	chr2:97483000-97484000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
41	chr2:97483000-97484000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:97483000-97484000	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr2:97483000-97484000	Flanking Active TSS	GM12878-XiMat	blood
44	chr2:97483000-97484200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:97483000-97484400	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr2:97483000-97484400	Flanking Active TSS	Fetal Thymus	thymus
47	chr2:97483000-97484800	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr2:97483000-97485200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
49	chr2:97483000-97485800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
50	chr2:97483000-97486600	Transcr. at gene 5' and 3'	Dnd41	blood

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