Variant report

Variant	rs3806615
Chromosome Location	chr3:100120269-100120270
allele	C/G
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	chr3:100119256-100121103	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:100119214-100121034	PBDE	blood:	n/a	n/a
3	POLR2A	chr3:100119234-100120974	Hela-S3	cervix:	n/a	n/a
4	TEAD4	chr3:100120107-100120487	H1-hESC	embryonic stem cell:	n/a	n/a
5	NR2F2	chr3:100119526-100120736	MCF-7	breast:	n/a	n/a
6	TCF7L2	chr3:100119737-100120759	HCT-116	colon:	n/a	n/a
7	EBF1	chr3:100120263-100120725	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:100119440-100120873	MCF-7	breast:	n/a	n/a
9	POLR2A	chr3:100119609-100121584	SK-N-SH	brain:	n/a	n/a
10	WRNIP1	chr3:100119876-100120980	GM12878	blood:	n/a	n/a
11	MAX	chr3:100119502-100120777	HCT-116	colon:	n/a	chr3:100120332-100120342
12	MAX	chr3:100119599-100120782	ECC-1	luminal epithelium:	n/a	chr3:100120332-100120342
13	NR2C2	chr3:100119341-100120716	GM12878	blood:	n/a	chr3:100119932-100119945 chr3:100120032-100120041
14	EGR1	chr3:100119839-100120414	GM12878	blood:	n/a	chr3:100120047-100120058 chr3:100120046-100120059 chr3:100120049-100120058 chr3:100120332-100120342 chr3:100120029-100120038 chr3:100120047-100120058 chr3:100120331-100120341 chr3:100120048-100120058 chr3:100120046-100120060 chr3:100120327-100120340 chr3:100120099-100120123 chr3:100120048-100120058 chr3:100120046-100120059
15	REST	chr3:100119602-100120823	HL-60	blood:	n/a	n/a
16	TAF1	chr3:100119654-100120634	K562	blood:	n/a	n/a
17	POLR2A	chr3:100118920-100121749	MCF10A-Er-Src	breast:	n/a	n/a
18	EGR1	chr3:100119747-100120394	ECC-1	luminal epithelium:	n/a	chr3:100120047-100120058 chr3:100120046-100120059 chr3:100120049-100120058 chr3:100120332-100120342 chr3:100120029-100120038 chr3:100120047-100120058 chr3:100120331-100120341 chr3:100120048-100120058 chr3:100120046-100120060 chr3:100120327-100120340 chr3:100120099-100120123 chr3:100120048-100120058 chr3:100120046-100120059
19	CREB1	chr3:100119559-100120607	A549	lung:	n/a	n/a
20	MXI1	chr3:100119341-100120820	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr3:100119532-100120442	ECC-1	luminal epithelium:	n/a	n/a
22	TAF1	chr3:100119673-100120550	HepG2	liver:	n/a	n/a
23	MAZ	chr3:100119719-100120874	K562	blood:	n/a	chr3:100120332-100120342
24	REST	chr3:100119709-100120774	A549	lung:	n/a	n/a
25	NFYA	chr3:100119867-100120633	GM12878	blood:	n/a	n/a
26	YY1	chr3:100119717-100120983	SK-N-SH	brain:	n/a	chr3:100120170-100120189
27	MAX	chr3:100119167-100120951	NB4	blood:	n/a	chr3:100120332-100120342
28	POLR2A	chr3:100118927-100121609	MCF10A-Er-Src	breast:	n/a	n/a
29	SP2	chr3:100120208-100120367	K562	blood:	n/a	n/a
30	PML	chr3:100119705-100120730	K562	blood:	n/a	n/a
31	YY1	chr3:100119381-100120884	HepG2	liver:	n/a	chr3:100120170-100120189
32	MAX	chr3:100119637-100120985	H1-hESC	embryonic stem cell:	n/a	chr3:100120332-100120342
33	POLR2A	chr3:100119253-100121011	HL-60	blood:	n/a	n/a
34	SIN3AK20	chr3:100119044-100120679	PANC-1	pancreas:	n/a	n/a
35	TAF1	chr3:100120129-100120530	A549	lung:	n/a	n/a
36	EBF1	chr3:100120040-100120750	GM12878	blood:	n/a	n/a
37	YY1	chr3:100120066-100120745	H1-hESC	embryonic stem cell:	n/a	chr3:100120170-100120189
38	TAF1	chr3:100119680-100120929	H1-neurons	neurons:	n/a	n/a
39	MYC	chr3:100119401-100120740	MCF-7	breast:	n/a	chr3:100120332-100120342
40	SP4	chr3:100119903-100120562	H1-hESC	embryonic stem cell:	n/a	chr3:100120281-100120292 chr3:100120202-100120213 chr3:100120329-100120345 chr3:100120327-100120343
41	STAT5A	chr3:100119628-100120946	GM12878	blood:	n/a	chr3:100120009-100120021
42	POLR2A	chr3:100118252-100121519	K562	blood:	n/a	n/a
43	MAFF	chr3:100119991-100120744	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:100119217-100120898	H1-neurons	neurons:	n/a	n/a
45	TAF1	chr3:100119709-100120690	PFSK-1	brain:	n/a	n/a
46	TCF12	chr3:100119676-100120429	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr3:100119351-100120939	GM15510	blood:	n/a	n/a
48	TRIM28	chr3:100119787-100120669	K562	blood:	n/a	n/a
49	POLR2A	chr3:100119710-100120952	GM12891	blood:	n/a	n/a
50	GABPA	chr3:100119710-100120342	HepG2	liver:	n/a	chr3:100120332-100120341

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:100120235-100120285	HCF	heart:	n/a
2	chr3:100120235-100120285	ProgFib	skin:	n/a
3	chr3:100120235-100120285	IMR90	lung:	fetal
4	chr3:100120235-100120285	H1-hESC	embryonic stem cell:	embryo
5	chr3:100120235-100120285	HCM	heart:	n/a
6	chr3:100120235-100120285	NT2-D1	testis:	n/a
7	chr3:100120235-100120285	U87	brain:	n/a
8	chr3:100120235-100120285	HEEpiC	esophagus:	n/a
9	chr3:100120235-100120285	HPAEpiC	pulmonary alveolar:	n/a
10	chr3:100120235-100120285	HIPEpiC	eye:	n/a
11	chr3:100120235-100120285	MCF-7	breast:	n/a
12	chr3:100120235-100120285	RPTEC	kidney:	n/a
13	chr3:100120235-100120285	GM12891	blood:	n/a
14	chr3:100120235-100120285	PFSK-1	brain:	n/a
15	chr3:100120235-100120285	NHBE	bronchial:	n/a
16	chr3:100120235-100120285	GM12878	blood:	n/a
17	chr3:100120235-100120285	HCT-116	colon:	n/a
18	chr3:100120235-100120285	HRCEpiC	kidney:	n/a
19	chr3:100120235-100120285	HepG2	liver:	n/a
20	chr3:100120235-100120285	MCF10A-Er-Src	breast:	n/a
21	chr3:100120235-100120285	A549	lung:	n/a
22	chr3:100120235-100120285	NB4	blood:	n/a
23	chr3:100120235-100120285	HUVEC	blood vessel:	n/a
24	chr3:100120235-100120285	HAEpiC	amniotic membrane:	n/a
25	chr3:100120235-100120285	AG10803	skin:	n/a
26	chr3:100120235-100120285	GM12892	blood:	n/a
27	chr3:100120235-100120285	SK-N-SH_RA	brain:	n/a
28	chr3:100120235-100120285	AG04450	lung:	fetal
29	chr3:100120235-100120285	HMEC	breast:	n/a
30	chr3:100120235-100120285	AG04449	skin:	fetal
31	chr3:100120235-100120285	HRE	kidney:	n/a
32	chr3:100120235-100120285	Caco-2	colon:	n/a
33	chr3:100120235-100120285	BJ	skin:	n/a
34	chr3:100120235-100120285	HEK293	kidney:	embryo
35	chr3:100120235-100120285	NH-A	brain:	n/a
36	chr3:100120235-100120285	LNCaP	prostate:	n/a
37	chr3:100120235-100120285	Jurkat	blood:	n/a
38	chr3:100120235-100120285	Hepatocyte	liver:	n/a
39	chr3:100120235-100120285	ECC-1	luminal epithelium:	n/a
40	chr3:100120235-100120285	SK-N-MC	brain:	n/a
41	chr3:100120235-100120285	AG09309	skin:	n/a
42	chr3:100120235-100120285	AoSMC	blood vessel:	n/a
43	chr3:100120235-100120285	SAEC	small airway:	n/a
44	chr3:100120235-100120285	K562	blood:	n/a
45	chr3:100120235-100120285	AG09319	gingival:	n/a
46	chr3:100120235-100120285	CMK	blood:	n/a
47	chr3:100120235-100120285	HRPEpiC	eye:	n/a
48	chr3:100120235-100120285	BE2_C	brain:	n/a
49	chr3:100120235-100120285	NHDF-neo	bronchial:	n/a
50	chr3:100120235-100120285	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:100079303..100082344-chr3:100118989..100121864,3	K562	blood:
2	chr3:100052074..100055881-chr3:100116822..100121530,5	MCF-7	breast:
3	chr12:49524673..49525578-chr3:100119638..100120570,2	NB4	blood:
4	chr3:100120119..100120883-chr4:140098243..140098989,2	NB4	blood:
5	chr3:100118702..100121299-chr3:100427057..100432444,4	K562	blood:
6	chr3:100033941..100036861-chr3:100119084..100121565,2	MCF-7	breast:
7	chr17:57182962..57185099-chr3:100120179..100122851,2	MCF-7	breast:
8	chr3:100119962..100120935-chr8:144635246..144635884,2	Hela-S3	cervix:
9	chr16:68270129..68270992-chr3:100120145..100120750,2	Hela-S3	cervix:
10	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
11	chr17:16118623..16119597-chr3:100120034..100120875,2	Hela-S3	cervix:
12	chr3:100118496..100120943-chr3:101229402..101232050,2	K562	blood:
13	chr3:99979418..99981870-chr3:100118340..100121144,2	K562	blood:
14	chr22:39928076..39928847-chr3:100119781..100120617,2	HCT-116	colon:
15	chr3:100119965..100120769-chr6:26056301..26057168,2	Hela-S3	cervix:
16	chr3:100119980..100121652-chr3:101394464..101397120,2	K562	blood:
17	chr1:161283919..161284697-chr3:100120243..100120839,2	Hela-S3	cervix:
18	chr3:99985781..99987839-chr3:100119283..100121257,2	K562	blood:
19	chr3:100099401..100103527-chr3:100117550..100121361,6	MCF-7	breast:
20	chr3:100056838..100058599-chr3:100119834..100121558,2	MCF-7	breast:
21	chr3:99535287..99537035-chr3:100119228..100122105,2	MCF-7	breast:
22	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:

Variant related genes	Relation type
LNP1	TF binding region
TOMM70A	TF binding region
TOMM70A	CpG island
LNP1	CpG island
ENSG00000066422	Chromatin interaction
ENSG00000114354	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000103067	Chromatin interaction
ENSG00000104518	Chromatin interaction
ENSG00000114021	Chromatin interaction
ENSG00000256628	Chromatin interaction
ENSG00000187051	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000138468	Chromatin interaction
ENSG00000109381	Chromatin interaction
ENSG00000036054	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000143252	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000154174	Chromatin interaction
ENSG00000273488	Chromatin interaction
ENSG00000184220	Chromatin interaction
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10936180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1123578	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1214380	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1214381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1228184	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12495001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1530283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs166747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs277620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs277622	0.91[ASN][1000 genomes]
rs277623	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs277626	0.93[ASN][1000 genomes]
rs277628	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs277629	0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs277630	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs277633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs277634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs277635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs277638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs277642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs277644	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs277651	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs372438	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3772692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs392066	0.83[AMR][1000 genomes]
rs402870	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs413425	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs431069	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs432715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6780662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs6791102	0.93[ASN][1000 genomes]
rs6794955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7616634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7641630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3806615	ENSG00000206535	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100116800-100121600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:100117000-100123000	Active TSS	K562	blood
3	chr3:100117600-100121000	Active TSS	Fetal Kidney	kidney
4	chr3:100117800-100122800	Active TSS	Right Atrium	heart
5	chr3:100118200-100122000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:100118200-100122000	Active TSS	Left Ventricle	heart
7	chr3:100118200-100122400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:100118200-100122400	Active TSS	HSMMtube	muscle
9	chr3:100118200-100122600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:100118200-100122600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:100118200-100123400	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:100118200-100123600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:100118400-100122600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:100118400-100122600	Active TSS	Fetal Intestine Large	intestine
15	chr3:100118400-100122600	Active TSS	NHDF-Ad	bronchial
16	chr3:100118400-100123000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:100118400-100123000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:100118400-100123000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:100118400-100123000	Active TSS	NHLF	lung
20	chr3:100118600-100120400	Active TSS	NH-A	brain
21	chr3:100118600-100121000	Active TSS	Gastric	stomach
22	chr3:100118600-100122000	Bivalent/Poised TSS	HepG2	liver
23	chr3:100118600-100123000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr3:100118800-100120800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:100118800-100120800	Active TSS	Small Intestine	intestine
26	chr3:100118800-100121000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:100118800-100121000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:100118800-100121000	Active TSS	Esophagus	oesophagus
29	chr3:100118800-100121600	Active TSS	A549	lung
30	chr3:100118800-100121600	Active TSS	HMEC	breast
31	chr3:100118800-100121800	Active TSS	Fetal Intestine Small	intestine
32	chr3:100118800-100121800	Active TSS	Ovary	ovary
33	chr3:100118800-100122000	Active TSS	Aorta	Aorta
34	chr3:100118800-100122000	Active TSS	Right Ventricle	heart
35	chr3:100118800-100122200	Active TSS	Fetal Lung	lung
36	chr3:100118800-100122200	Active TSS	Fetal Stomach	stomach
37	chr3:100118800-100122400	Active TSS	Colonic Mucosa	Colon
38	chr3:100118800-100122600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:100118800-100122600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:100118800-100122600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:100118800-100123000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:100118800-100123400	Active TSS	GM12878-XiMat	blood
43	chr3:100119000-100120600	Active TSS	NHEK	skin
44	chr3:100119000-100120800	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr3:100119000-100120800	Active TSS	Spleen	Spleen
46	chr3:100119000-100121000	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr3:100119000-100121000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:100119000-100121000	Active TSS	Lung	lung
49	chr3:100119000-100121000	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr3:100119000-100121200	Active TSS	Muscle Satellite Cultured Cells	--

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