Variant report

Variant	rs4768692
Chromosome Location	chr12:46639635-46639636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46383357..46385592-chr12:46637967..46640337,2	MCF-7	breast:
2	chr12:46638042..46640582-chr12:46776213..46778241,2	K562	blood:
3	chr12:46626606..46630930-chr12:46637487..46640302,3	K562	blood:
4	chr12:46636917..46639849-chr12:46653348..46655689,2	MCF-7	breast:
5	chr12:46639144..46640691-chr12:46658808..46661805,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257261	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1000405	0.89[EUR][1000 genomes]
rs10880944	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11504510	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12303214	0.96[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12320197	0.84[CHD][hapmap]
rs12580460	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492893	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492897	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2408495	0.86[EUR][1000 genomes]
rs3847985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4445700	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768109	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768693	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56988021	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312682	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957777	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7959095	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7960819	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7967629	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971312	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs973988	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46592800-46654200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:46597600-46659600	Weak transcription	Colonic Mucosa	Colon
3	chr12:46610600-46640000	Weak transcription	Esophagus	oesophagus
4	chr12:46613800-46639800	Weak transcription	Lung	lung
5	chr12:46615800-46653800	Weak transcription	NH-A	brain
6	chr12:46616000-46640600	Strong transcription	Fetal Thymus	thymus
7	chr12:46616000-46650400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:46616400-46653600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:46616800-46639800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:46616800-46641600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:46617000-46653000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:46617200-46640200	Strong transcription	Hela-S3	cervix
13	chr12:46618400-46639800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:46618400-46639800	Weak transcription	Spleen	Spleen
15	chr12:46618400-46641400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:46618400-46653800	Weak transcription	HSMMtube	muscle
17	chr12:46618600-46639800	Weak transcription	Aorta	Aorta
18	chr12:46619400-46639800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:46619600-46639800	Weak transcription	Psoas Muscle	Psoas
20	chr12:46622400-46649600	Weak transcription	Small Intestine	intestine
21	chr12:46622400-46650800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:46627800-46639800	Weak transcription	Right Atrium	heart
23	chr12:46627800-46640000	Weak transcription	Gastric	stomach
24	chr12:46628200-46640000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:46629400-46650600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:46629600-46650400	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:46629800-46640400	Strong transcription	NHEK	skin
28	chr12:46632800-46650800	Weak transcription	Brain Germinal Matrix	brain
29	chr12:46633000-46639800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:46633600-46647400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:46633600-46653800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:46634000-46639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:46634800-46640200	Weak transcription	Fetal Intestine Large	intestine
34	chr12:46635000-46640400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:46635200-46653600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:46635600-46647400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:46635600-46654000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:46635600-46660000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:46635800-46646000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:46635800-46653800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:46636000-46640400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:46636000-46647400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:46636200-46640600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr12:46636600-46639800	Weak transcription	Thymus	Thymus
45	chr12:46636600-46640000	Weak transcription	Placenta	Placenta
46	chr12:46636800-46639800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:46636800-46646000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:46637000-46640200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr12:46637200-46640400	ZNF genes & repeats	A549	lung
50	chr12:46637200-46640600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--

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