Variant report

Variant	rs1871197
Chromosome Location	chr19:38146773-38146774
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	MYC	chr19:38146769-38147173	MCF-7	breast:	n/a	n/a
2	NRF1	chr19:38146079-38146920	Hela-S3	cervix:	n/a	chr19:38146748-38146762 chr19:38146696-38146705 chr19:38146751-38146765 chr19:38146402-38146411 chr19:38146751-38146760 chr19:38146750-38146761 chr19:38146758-38146767 chr19:38146751-38146762
3	POLR2A	chr19:38145479-38147391	HepG2	liver:	n/a	n/a
4	IRF1	chr19:38146767-38147174	K562	blood:	n/a	n/a
5	PML	chr19:38146702-38147025	GM12878	blood:	n/a	n/a
6	TAF1	chr19:38146163-38147341	H1-neurons	neurons:	n/a	n/a
7	FOXA1	chr19:38146713-38147195	HepG2	liver:	n/a	n/a
8	STAT5A	chr19:38146548-38147205	GM12878	blood:	n/a	chr19:38146691-38146703
9	ZMIZ1	chr19:38146017-38147202	K562	blood:	n/a	n/a
10	TAF1	chr19:38145897-38147193	ECC-1	luminal epithelium:	n/a	n/a
11	ELF1	chr19:38146151-38146806	GM12878	blood:	n/a	n/a
12	TCF3	chr19:38146601-38147180	GM12878	blood:	n/a	n/a
13	CHD2	chr19:38145886-38147414	K562	blood:	n/a	chr19:38146694-38146704
14	JUND	chr19:38146600-38147259	A549	lung:	n/a	chr19:38147142-38147153 chr19:38146692-38146701
15	CUX1	chr19:38146739-38146835	K562	blood:	n/a	n/a
16	MAX	chr19:38145396-38147330	MCF-7	breast:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
17	POLR2A	chr19:38146093-38147229	HepG2	liver:	n/a	n/a
18	UBTF	chr19:38145350-38147258	K562	blood:	n/a	n/a
19	MAX	chr19:38145158-38147468	A549	lung:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
20	POLR2A	chr19:38145570-38147379	HL-60	blood:	n/a	n/a
21	E2F6	chr19:38145832-38147266	K562	blood:	n/a	chr19:38147005-38147014 chr19:38146696-38146705 chr19:38146752-38146761
22	POLR2A	chr19:38145969-38147172	A549	lung:	n/a	n/a
23	POLR2A	chr19:38145482-38146938	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr19:38146653-38147218	GM12878	blood:	n/a	n/a
25	GATA2	chr19:38145898-38147392	SH-SY5Y	brain:	n/a	n/a
26	TAF1	chr19:38145639-38147300	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:38146636-38147187	A549	lung:	n/a	n/a
28	POU2F2	chr19:38146665-38147287	GM12878	blood:	n/a	chr19:38146696-38146708
29	UBTF	chr19:38145491-38147030	K562	blood:	n/a	n/a
30	BHLHE40	chr19:38146164-38147269	HepG2	liver:	n/a	chr19:38146433-38146449 chr19:38146999-38147015
31	POLR2A	chr19:38146727-38147221	H1-hESC	embryonic stem cell:	n/a	n/a
32	CHD2	chr19:38146063-38147264	HepG2	liver:	n/a	chr19:38146694-38146704
33	CEBPB	chr19:38146031-38147033	Hela-S3	cervix:	n/a	n/a
34	REST	chr19:38146104-38147547	H1-neurons	neurons:	n/a	chr19:38146308-38146321 chr19:38146695-38146708
35	POLR2A	chr19:38146656-38147250	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:38146006-38146856	K562	blood:	n/a	n/a
37	ZKSCAN1	chr19:38145626-38147205	Hela-S3	cervix:	n/a	chr19:38146327-38146340
38	BHLHE40	chr19:38145729-38147344	K562	blood:	n/a	chr19:38146433-38146449 chr19:38146999-38147015
39	NRF1	chr19:38145869-38147564	SK-N-SH	brain:	n/a	chr19:38146748-38146762 chr19:38146696-38146705 chr19:38146751-38146765 chr19:38146402-38146411 chr19:38146751-38146760 chr19:38146750-38146761 chr19:38146758-38146767 chr19:38146751-38146762 chr19:38147005-38147014
40	FOXA1	chr19:38146694-38147234	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:38145510-38147461	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr19:38145590-38147291	MCF-7	breast:	n/a	n/a
43	TBP	chr19:38146081-38147264	HepG2	liver:	n/a	n/a
44	MAZ	chr19:38145365-38147377	IMR90	lung:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
45	ZNF384	chr19:38146387-38147061	K562	blood:	n/a	n/a
46	POLR2A	chr19:38146725-38146915	K562	blood:	n/a	n/a
47	POLR2A	chr19:38146142-38147177	HEK293	kidney:	n/a	n/a
48	MYC	chr19:38146723-38147208	MCF-7	breast:	n/a	n/a
49	MAX	chr19:38145131-38147074	Hela-S3	cervix:	n/a	chr19:38146453-38146462 chr19:38146550-38146559
50	POLR2A	chr19:38145503-38147263	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75932176..75933046-chr19:38146017..38146882,2	Hela-S3	cervix:
2	chr19:38145174..38146985-chr19:38184008..38186251,2	MCF-7	breast:
3	chr19:38085961..38087829-chr19:38145172..38147580,2	K562	blood:
4	chr19:37957663..37960695-chr19:38143642..38147199,3	MCF-7	breast:
5	chr19:37958940..37961916-chr19:38146231..38147953,2	K562	blood:
6	chr19:37960304..37962188-chr19:38144303..38146867,2	MCF-7	breast:

Variant related genes	Relation type
ZFP30	TF binding region
ENSG00000171827	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000171817	Chromatin interaction
ENSG00000196437	Chromatin interaction
ENSG00000267319	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1038084	0.89[CEU][hapmap]
rs1038085	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10407657	0.84[CEU][hapmap]
rs10417204	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10424612	0.89[CEU][hapmap]
rs10425671	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11665877	0.91[EUR][1000 genomes]
rs11667454	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667457	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668434	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11668558	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11670655	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883392	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1236810	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12972712	0.91[EUR][1000 genomes]
rs12981237	0.91[EUR][1000 genomes]
rs12982288	0.91[EUR][1000 genomes]
rs12983298	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17306508	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs17306795	1.00[CHB][hapmap]
rs2045909	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2126978	0.84[CEU][hapmap]
rs2160640	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2199644	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291000	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385116	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385124	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385125	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs241937	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs241940	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs241941	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs241942	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs241947	0.87[EUR][1000 genomes]
rs241948	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs241951	1.00[CHB][hapmap]
rs241953	0.86[EUR][1000 genomes]
rs241959	0.81[EUR][1000 genomes]
rs241960	0.81[EUR][1000 genomes]
rs2617789	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2909106	0.85[EUR][1000 genomes]
rs2927741	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927744	0.84[CEU][hapmap]
rs2972453	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972454	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112435	0.91[EUR][1000 genomes]
rs34351186	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34607899	0.93[EUR][1000 genomes]
rs34782935	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34949193	0.86[EUR][1000 genomes]
rs35015599	0.91[EUR][1000 genomes]
rs35214625	0.91[EUR][1000 genomes]
rs35273320	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35415221	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36020184	0.90[EUR][1000 genomes]
rs36092052	0.90[EUR][1000 genomes]
rs3752365	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4273159	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4482404	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4802066	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802069	0.84[CEU][hapmap]
rs4802134	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4803216	0.89[CEU][hapmap]
rs4803228	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57308437	0.91[EUR][1000 genomes]
rs62108304	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108339	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62108355	0.90[EUR][1000 genomes]
rs6508729	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6508738	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251097	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7253174	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254170	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254828	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs7255283	0.84[CEU][hapmap]
rs8111055	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8113076	0.84[CEU][hapmap]
rs856302	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38144000-38148000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:38144200-38147200	Active TSS	GM12878-XiMat	blood
3	chr19:38144400-38147600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38144600-38146800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:38144600-38147000	Active TSS	A549	lung
6	chr19:38144600-38147200	Active TSS	Fetal Kidney	kidney
7	chr19:38144600-38147400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:38144600-38147400	Active TSS	NHDF-Ad	bronchial
9	chr19:38144600-38147600	Active TSS	Fetal Stomach	stomach
10	chr19:38144600-38147600	Active TSS	Hela-S3	cervix
11	chr19:38144600-38147600	Active TSS	NHLF	lung
12	chr19:38144800-38147200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr19:38144800-38147200	Active TSS	Fetal Thymus	thymus
14	chr19:38144800-38147400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:38144800-38147400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:38144800-38147400	Active TSS	Left Ventricle	heart
17	chr19:38144800-38147600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr19:38144800-38147600	Active TSS	H1 Cell Line	embryonic stem cell
19	chr19:38144800-38147600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:38144800-38147600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:38144800-38147600	Active TSS	Fetal Muscle Trunk	muscle
22	chr19:38145000-38147000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:38145000-38147000	Active TSS	Right Ventricle	heart
24	chr19:38145000-38147000	Active TSS	Stomach Smooth Muscle	stomach
25	chr19:38145000-38147200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:38145000-38147200	Active TSS	Muscle Satellite Cultured Cells	--
27	chr19:38145000-38147200	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr19:38145000-38147200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:38145000-38147200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:38145000-38147400	Active TSS	Ovary	ovary
31	chr19:38145000-38147400	Active TSS	Right Atrium	heart
32	chr19:38145000-38147600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr19:38145000-38147600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr19:38145000-38147600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:38145000-38147600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:38145000-38147600	Active TSS	Fetal Intestine Large	intestine
37	chr19:38145000-38147600	Active TSS	Psoas Muscle	Psoas
38	chr19:38145000-38147600	Active TSS	HSMM	muscle
39	chr19:38145000-38147600	Active TSS	HSMMtube	muscle
40	chr19:38145000-38147800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:38145200-38147000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:38145200-38147000	Active TSS	Placenta	Placenta
43	chr19:38145200-38147200	Active TSS	Colon Smooth Muscle	Colon
44	chr19:38145200-38147200	Active TSS	Fetal Lung	lung
45	chr19:38145200-38147200	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr19:38145200-38147200	Active TSS	Thymus	Thymus
47	chr19:38145200-38147200	Active TSS	Dnd41	blood
48	chr19:38145200-38147200	Active TSS	NHEK	skin
49	chr19:38145200-38147400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr19:38145200-38147400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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