Variant report

Variant	rs1694408
Chromosome Location	chr1:76254139-76254140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
2	POLR2A	chr1:76253830-76254234	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:76253948-76254266	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
5	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
7	POLR2A	chr1:76251073-76257428	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:76253826-76254221	K562	blood:	n/a	n/a
9	HEY1	chr1:76253258-76254146	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:76251198-76257365	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:76251042-76257307	U87	brain:	n/a	n/a
12	POLR2A	chr1:76253821-76254160	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:76250200-76254234	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:76253758-76254198	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:76250130-76254424	K562	blood:	n/a	n/a
16	POLR2A	chr1:76253821-76254216	GM12891	blood:	n/a	n/a
17	POLR2A	chr1:76251041-76254344	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:76250277-76254427	GM12892	blood:	n/a	n/a
20	POLR2A	chr1:76251108-76257452	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:76251241-76254471	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr1:76253946-76254234	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:76253785-76254199	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:76253912-76254412	GM12891	blood:	n/a	n/a
25	TEAD4	chr1:76254009-76254211	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
27	POLR2A	chr1:76253921-76254214	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:76250320-76254265	GM18526	blood:	n/a	n/a
29	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
30	TBL1XR1	chr1:76249814-76254171	K562	blood:	n/a	n/a
31	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
32	POLR2A	chr1:76253762-76254344	HCT-116	colon:	n/a	n/a
33	POLR2A	chr1:76253958-76254170	GM12878	blood:	n/a	n/a
34	CHD1	chr1:76251834-76255268	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:76250313-76254244	GM18951	blood:	n/a	n/a
36	POLR2A	chr1:76250200-76257400	GM19099	blood:	n/a	n/a
37	POLR2A	chr1:76253843-76254385	K562	blood:	n/a	n/a
38	POLR2A	chr1:76253757-76254321	GM12878	blood:	n/a	n/a
39	HEY1	chr1:76252696-76254266	K562	blood:	n/a	n/a
40	POLR2A	chr1:76251210-76255410	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:76250996-76257615	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:76251203-76256991	PFSK-1	brain:	n/a	n/a
43	HEY1	chr1:76253770-76254433	HepG2	liver:	n/a	n/a
44	POLR2A	chr1:76250185-76257476	GM12892	blood:	n/a	n/a
45	POLR2A	chr1:76251241-76256430	U87	brain:	n/a	n/a
46	CHD1	chr1:76251288-76254995	IMR90	lung:	n/a	n/a
47	POLR2A	chr1:76252677-76254213	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr1:76251070-76254368	SK-N-MC	brain:	n/a	n/a
49	POLR2A	chr1:76252995-76255924	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr1:76251178-76254176	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76252156..76254487-chr1:76258379..76261694,3	MCF-7	breast:
2	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
3	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
4	chr1:76195849..76201919-chr1:76251987..76255873,8	K562	blood:
5	chr1:76197028..76199654-chr1:76253368..76256114,2	K562	blood:
6	chr1:75197237..75200127-chr1:76254006..76255529,2	K562	blood:

No data

Variant related genes	Relation type
SNORD45B	TF binding region
RABGGTB	TF binding region
ENSG00000117054	Chromatin interaction
ENSG00000116791	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000178193	Chromatin interaction
ENSG00000162623	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1021463	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1068884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10747330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10873726	1.00[EUR][1000 genomes]
rs10873786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1093007	1.00[EUR][1000 genomes]
rs1093010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11161785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11161801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144335	1.00[EUR][1000 genomes]
rs1146575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146578	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146585	1.00[EUR][1000 genomes]
rs1146586	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146589	1.00[EUR][1000 genomes]
rs1146595	1.00[EUR][1000 genomes]
rs1146596	1.00[EUR][1000 genomes]
rs1146597	1.00[EUR][1000 genomes]
rs1146599	1.00[EUR][1000 genomes]
rs1146600	1.00[EUR][1000 genomes]
rs1146601	1.00[EUR][1000 genomes]
rs1146604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146621	1.00[EUR][1000 genomes]
rs1146633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146640	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1250879	1.00[EUR][1000 genomes]
rs1251066	1.00[EUR][1000 genomes]
rs1251074	1.00[EUR][1000 genomes]
rs1251271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1251532	1.00[EUR][1000 genomes]
rs1251538	1.00[EUR][1000 genomes]
rs1251554	1.00[EUR][1000 genomes]
rs1251559	1.00[EUR][1000 genomes]
rs1251563	1.00[EUR][1000 genomes]
rs1251585	1.00[AMR][1000 genomes]
rs1251589	1.00[EUR][1000 genomes]
rs1251590	1.00[EUR][1000 genomes]
rs1251592	1.00[EUR][1000 genomes]
rs1251593	1.00[EUR][1000 genomes]
rs1469988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1565718	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1565719	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1591119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1616175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1658743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1694423	1.00[EUR][1000 genomes]
rs1759276	1.00[AMR][1000 genomes]
rs1770514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1770884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1873895	1.00[AMR][1000 genomes]
rs211714	1.00[EUR][1000 genomes]
rs211720	1.00[EUR][1000 genomes]
rs211734	1.00[EUR][1000 genomes]
rs211735	1.00[EUR][1000 genomes]
rs211738	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs211739	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2347963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3119821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs381183	1.00[EUR][1000 genomes]
rs392695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs445008	1.00[EUR][1000 genomes]
rs699684	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs699685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs699686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs699687	1.00[EUR][1000 genomes]
rs699688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs699689	1.00[EUR][1000 genomes]
rs699823	1.00[EUR][1000 genomes]
rs699826	1.00[EUR][1000 genomes]
rs7541791	1.00[EUR][1000 genomes]
rs814846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs814852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs814854	1.00[EUR][1000 genomes]
rs815300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs815302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs815312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs865263	1.00[AMR][1000 genomes]
rs9437227	1.00[EUR][1000 genomes]
rs946982	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 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	chr1:76250400-76254800	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr1:76251000-76255200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:76251000-76255400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:76251200-76254600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:76251200-76254600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:76251200-76254600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:76251200-76254600	Active TSS	A549	lung
8	chr1:76251200-76255000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:76251200-76255000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:76251200-76255400	Active TSS	Right Atrium	heart
11	chr1:76251200-76256200	Active TSS	Right Ventricle	heart
12	chr1:76251400-76254400	Active TSS	Small Intestine	intestine
13	chr1:76251400-76254800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:76251600-76254800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:76251600-76254800	Active TSS	NHLF	lung
16	chr1:76252200-76258400	Weak transcription	Spleen	Spleen
17	chr1:76252400-76254600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:76252400-76255200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr1:76252400-76258800	Transcr. at gene 5' and 3'	K562	blood
20	chr1:76252600-76254800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:76252600-76257600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:76252800-76254200	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr1:76252800-76254200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:76252800-76254200	Flanking Active TSS	Fetal Brain Male	brain
25	chr1:76252800-76254400	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr1:76252800-76254800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr1:76252800-76254800	Flanking Active TSS	Liver	Liver
28	chr1:76252800-76255000	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:76252800-76255200	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr1:76252800-76256000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
31	chr1:76252800-76256800	Transcr. at gene 5' and 3'	Dnd41	blood
32	chr1:76252800-76257000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
33	chr1:76252800-76257000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:76252800-76257200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
35	chr1:76253000-76255200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
36	chr1:76253000-76255200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:76253000-76255400	Transcr. at gene 5' and 3'	HSMM	muscle
38	chr1:76253000-76255600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:76253000-76255800	Transcr. at gene 5' and 3'	HMEC	breast
40	chr1:76253000-76256000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
41	chr1:76253000-76256800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
42	chr1:76253000-76257400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
43	chr1:76253200-76254200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:76253200-76254200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
45	chr1:76253200-76254200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr1:76253200-76254200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:76253200-76254400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr1:76253200-76254400	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr1:76253200-76255200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:76253200-76255200	Enhancers	Primary neutrophils fromperipheralblood	blood

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