Variant report

Variant	rs12034397
Chromosome Location	chr1:95700267-95700268
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	RCOR1	chr1:95698181-95700584	IMR90	lung:	n/a	n/a
2	POLR2A	chr1:95699278-95700285	Hela-S3	cervix:	n/a	n/a
3	ZBTB7A	chr1:95699407-95700490	ECC-1	luminal epithelium:	n/a	chr1:95700126-95700134
4	MAZ	chr1:95698762-95700551	IMR90	lung:	n/a	chr1:95700157-95700167
5	POLR2A	chr1:95699404-95700416	K562	blood:	n/a	n/a
6	MYC	chr1:95700239-95700413	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr1:95700180-95700330	AG04449	skin:	n/a	chr1:95700208-95700218
8	POLR2A	chr1:95699259-95700288	K562	blood:	n/a	n/a
9	POLR2A	chr1:95698945-95700437	K562	blood:	n/a	n/a
10	POLR2A	chr1:95699430-95700399	GM18951	blood:	n/a	n/a
11	POLR2A	chr1:95699358-95700418	GM19099	blood:	n/a	n/a
12	POLR2A	chr1:95698513-95700286	HepG2	liver:	n/a	n/a
13	CTCF	chr1:95700260-95700410	BJ	skin:	n/a	n/a
14	EGR1	chr1:95700017-95700322	K562	blood:	n/a	chr1:95700201-95700223 chr1:95700135-95700144 chr1:95700206-95700219 chr1:95700120-95700130
15	MXI1	chr1:95698789-95700296	HepG2	liver:	n/a	n/a
16	RAD21	chr1:95699032-95700729	SK-N-SH	brain:	n/a	chr1:95700083-95700096
17	MAZ	chr1:95699460-95700442	HepG2	liver:	n/a	chr1:95700157-95700167
18	YY1	chr1:95699326-95700373	SK-N-SH	brain:	n/a	chr1:95699733-95699747
19	ZBTB7A	chr1:95699452-95700313	ECC-1	luminal epithelium:	n/a	chr1:95700126-95700134
20	POLR2A	chr1:95699315-95700301	K562	blood:	n/a	n/a
21	REST	chr1:95699464-95700375	H1-neurons	neurons:	n/a	chr1:95700262-95700280 chr1:95699886-95699899
22	POLR2A	chr1:95699339-95700307	GM12878	blood:	n/a	n/a
23	MAZ	chr1:95699424-95700318	Hela-S3	cervix:	n/a	chr1:95700157-95700167
24	MAZ	chr1:95699216-95700412	K562	blood:	n/a	chr1:95700157-95700167
25	POLR2A	chr1:95699335-95700269	GM18526	blood:	n/a	n/a
26	EGR1	chr1:95700088-95700302	K562	blood:	n/a	chr1:95700201-95700223 chr1:95700135-95700144 chr1:95700206-95700219 chr1:95700120-95700130
27	POLR2A	chr1:95699357-95700596	GM12891	blood:	n/a	n/a
28	HCFC1	chr1:95699096-95700306	Hela-S3	cervix:	n/a	n/a
29	MYC	chr1:95699218-95700327	K562	blood:	n/a	chr1:95700157-95700167
30	YY1	chr1:95699442-95700360	GM12878	blood:	n/a	chr1:95699733-95699747
31	CTCF	chr1:95699286-95700608	SK-N-SH	brain:	n/a	chr1:95700208-95700218
32	SMC3	chr1:95699168-95700515	SK-N-SH	brain:	n/a	chr1:95700035-95700045
33	POLR2A	chr1:95699350-95700404	GM18505	blood:	n/a	n/a
34	POLR2A	chr1:95700246-95700268	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:95699396-95700283	GM15510	blood:	n/a	n/a
36	MYC	chr1:95699354-95700433	K562	blood:	n/a	chr1:95700157-95700167
37	E2F6	chr1:95699281-95700400	K562	blood:	n/a	chr1:95699734-95699744
38	ZBTB7A	chr1:95700093-95700293	HepG2	liver:	n/a	chr1:95700126-95700134
39	NR2F2	chr1:95699557-95700461	K562	blood:	n/a	n/a
40	POLR2A	chr1:95699415-95700388	GM12892	blood:	n/a	n/a
41	CCNT2	chr1:95699329-95700375	K562	blood:	n/a	n/a
42	RCOR1	chr1:95700225-95700420	Hela-S3	cervix:	n/a	n/a
43	MAX	chr1:95698787-95700470	K562	blood:	n/a	chr1:95700157-95700167
44	CBX3	chr1:95700187-95700523	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:95581745..95584156-chr1:95699309..95702187,2	MCF-7	breast:
2	chr1:95699987..95702820-chr1:95708851..95710565,2	MCF-7	breast:
3	chr1:95581571..95584597-chr1:95698513..95700535,3	MCF-7	breast:
4	chr1:95582616..95585939-chr1:95698259..95700506,4	K562	blood:
5	chr1:95699874..95700489-chr3:68738675..68739508,2	HCT-116	colon:
6	chr1:95536810..95539827-chr1:95698878..95701315,3	K562	blood:
7	chr1:95582556..95585358-chr1:95698094..95701319,5	K562	blood:
8	chr1:95537299..95540042-chr1:95699496..95701047,2	K562	blood:

Variant related genes	Relation type
ENSG00000226026	TF binding region
ENSG00000271092	Chromatin interaction
ENSG00000231992	Chromatin interaction
ENSG00000152078	Chromatin interaction
ENSG00000172339	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10874906	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10874908	0.99[ASN][1000 genomes]
rs11165317	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11165318	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11165319	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11165333	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11165343	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11165346	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165349	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12021650	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12036706	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12037572	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12048133	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12085822	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12401359	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12407571	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12408858	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1927043	0.92[ASN][1000 genomes]
rs2147587	0.98[ASN][1000 genomes]
rs2148797	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2296308	0.98[ASN][1000 genomes]
rs259340	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259341	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259353	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259356	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738170	0.93[ASN][1000 genomes]
rs3738171	0.99[ASN][1000 genomes]
rs3753872	0.99[ASN][1000 genomes]
rs3767313	0.98[ASN][1000 genomes]
rs3767315	0.98[ASN][1000 genomes]
rs3820345	0.98[ASN][1000 genomes]
rs4950024	0.98[ASN][1000 genomes]
rs547339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs564610	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs592097	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61771764	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61771765	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61771766	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs658018	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6666528	0.98[ASN][1000 genomes]
rs6671408	0.99[ASN][1000 genomes]
rs688633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528790	0.97[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	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 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	chr1:95698200-95700400	Active TSS	Aorta	Aorta
2	chr1:95698200-95700600	Active TSS	Colon Smooth Muscle	Colon
3	chr1:95698200-95700600	Active TSS	Ovary	ovary
4	chr1:95698200-95700600	Active TSS	Right Atrium	heart
5	chr1:95698200-95700600	Active TSS	A549	lung
6	chr1:95698400-95700400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:95698400-95700600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:95698400-95700600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:95698400-95700600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr1:95698400-95700600	Active TSS	Fetal Kidney	kidney
11	chr1:95698400-95700600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:95698600-95700400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:95698600-95700600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:95698600-95700600	Active TSS	Brain Anterior Caudate	brain
15	chr1:95698600-95700600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:95698600-95700600	Active TSS	Fetal Intestine Large	intestine
17	chr1:95698600-95700600	Active TSS	Right Ventricle	heart
18	chr1:95698600-95700600	Active TSS	NHDF-Ad	bronchial
19	chr1:95698800-95700400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:95698800-95700400	Active TSS	Brain Substantia Nigra	brain
21	chr1:95698800-95700400	Active TSS	Colonic Mucosa	Colon
22	chr1:95698800-95700400	Active TSS	Esophagus	oesophagus
23	chr1:95698800-95700400	Active TSS	Gastric	stomach
24	chr1:95698800-95700400	Active TSS	Left Ventricle	heart
25	chr1:95698800-95700400	Active TSS	Placenta Amnion	Placenta Amnion
26	chr1:95698800-95700400	Active TSS	Psoas Muscle	Psoas
27	chr1:95698800-95700600	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:95698800-95700600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:95698800-95700600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr1:95698800-95700600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr1:95698800-95700600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr1:95698800-95700600	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:95698800-95700600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:95698800-95700600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:95698800-95700600	Active TSS	Fetal Brain Female	brain
36	chr1:95698800-95700600	Active TSS	Fetal Intestine Small	intestine
37	chr1:95698800-95700600	Active TSS	Rectal Smooth Muscle	rectum
38	chr1:95698800-95700600	Active TSS	HepG2	liver
39	chr1:95699000-95700400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:95699000-95700400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:95699000-95700400	Active TSS	Brain Hippocampus Middle	brain
42	chr1:95699000-95700400	Active TSS	Small Intestine	intestine
43	chr1:95699000-95700400	Active TSS	Spleen	Spleen
44	chr1:95699000-95700600	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:95699000-95700600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:95699000-95700600	Active TSS	NHLF	lung
47	chr1:95699000-95700800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:95699200-95700400	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr1:95699200-95700400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:95699200-95700400	Active TSS	Duodenum Mucosa	Duodenum

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