Variant report

Variant	rs12035647
Chromosome Location	chr1:212487311-212487312
allele	A/C
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	TCF12	chr1:212486950-212487492	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr1:212486964-212487501	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr1:212486890-212487406	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212487148..212489947-chr1:212490208..212492615,2	K562	blood:
2	chr1:212486882..212489433-chr1:212500849..212503303,2	K562	blood:
3	chr1:212207316..212210086-chr1:212486077..212488983,2	MCF-7	breast:
4	chr1:212480848..212483248-chr1:212485373..212487315,2	K562	blood:

Variant related genes	Relation type
ENSG00000225338	TF binding region
ENSG00000143493	Chromatin interaction
ENSG00000143476	Chromatin interaction
ENSG00000225338	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11119904	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12023488	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12024665	0.89[ASN][1000 genomes]
rs12033246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036130	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12410664	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1389371	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs17042034	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1774249	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992643	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2252044	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2298114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2516331	0.82[EUR][1000 genomes]
rs2589474	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3099112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs351373	0.82[EUR][1000 genomes]
rs351377	0.82[EUR][1000 genomes]
rs351378	0.82[EUR][1000 genomes]
rs351379	0.82[EUR][1000 genomes]
rs351380	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351386	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs351393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351398	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351401	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs351407	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351408	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351417	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs351419	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3767861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767863	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951582	0.81[EUR][1000 genomes]
rs4951588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4951589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6659594	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs701905	0.84[YRI][hapmap]
rs7415843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7519959	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7521853	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544225	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs792445	0.86[EUR][1000 genomes]
rs792447	0.84[YRI][hapmap]
rs792448	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1806604	chr1:212468974-212505860	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12035647	NENF	cis	Esophagus Mucosa	GTEx
rs12035647	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs12035647	TMEM206	cis	Esophagus Mucosa	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
2	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
3	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:212466600-212503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:212467400-212526000	Weak transcription	A549	lung
6	chr1:212474200-212502800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:212474600-212489200	Weak transcription	Gastric	stomach
8	chr1:212475600-212488600	Weak transcription	Fetal Heart	heart
9	chr1:212478200-212495800	Weak transcription	Fetal Thymus	thymus
10	chr1:212479200-212525400	Weak transcription	Aorta	Aorta
11	chr1:212479600-212489000	Weak transcription	Small Intestine	intestine
12	chr1:212479600-212489200	Weak transcription	Stomach Mucosa	stomach
13	chr1:212480600-212489400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:212480800-212488400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:212481600-212488600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:212482600-212488800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:212483400-212488000	Enhancers	NHDF-Ad	bronchial
18	chr1:212483400-212489400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:212483800-212487800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:212483800-212489200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:212484000-212487600	Strong transcription	Primary B cells from cord blood	blood
22	chr1:212484000-212487600	Enhancers	Osteobl	bone
23	chr1:212484000-212503000	Weak transcription	Fetal Stomach	stomach
24	chr1:212484000-212506600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:212484200-212487400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:212484200-212487400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:212484200-212487800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:212484200-212488600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:212484200-212488600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:212484200-212489000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:212484200-212489200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:212484200-212493400	Weak transcription	K562	blood
33	chr1:212484200-212507000	Weak transcription	HepG2	liver
34	chr1:212484400-212488000	Weak transcription	Psoas Muscle	Psoas
35	chr1:212484400-212488200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:212484400-212488600	Weak transcription	Brain Substantia Nigra	brain
37	chr1:212484400-212488800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:212484400-212488800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:212484400-212489000	Weak transcription	Liver	Liver
40	chr1:212484400-212489200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:212484400-212489200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:212484400-212489200	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:212484400-212489200	Weak transcription	Right Atrium	heart
44	chr1:212484400-212489400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:212484400-212489600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:212484400-212489600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:212484400-212489600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:212484400-212490400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr1:212484400-212493400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:212484400-212496200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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