Variant report

Variant	rs12986917
Chromosome Location	chr2:173972785-173972786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173972593..173975547-chr2:173981865..173984989,3	MCF-7	breast:
2	chr2:173972338..173974560-chr2:173994516..173997449,2	K562	blood:
3	chr2:173954752..173958851-chr2:173972387..173974213,3	K562	blood:
4	chr2:173965020..173969595-chr2:173970768..173975249,5	K562	blood:
5	chr2:173938768..173940892-chr2:173972337..173974150,2	K562	blood:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10187560	0.86[CHD][hapmap]
rs10930579	0.81[ASN][1000 genomes]
rs12615166	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12616714	0.81[ASN][1000 genomes]
rs12987496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12989116	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997078	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12998711	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13004212	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13017210	0.83[AFR][1000 genomes]
rs13017438	0.81[ASN][1000 genomes]
rs13022800	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13029949	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13032010	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs16861272	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16861278	0.89[CHB][hapmap]
rs17302977	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17761169	0.82[CHB][hapmap]
rs2076857	0.86[ASN][1000 genomes]
rs2278883	0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs2289397	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs2289399	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs34472765	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34681024	0.83[ASN][1000 genomes]
rs34702663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34862313	0.82[AMR][1000 genomes]
rs35250703	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35599077	0.83[ASN][1000 genomes]
rs36102078	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36103648	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3754741	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs3754743	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3754744	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3769161	0.88[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3769167	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3769187	1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3769192	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3769194	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769199	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3769203	0.87[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4972533	0.82[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap]
rs55913048	0.81[ASN][1000 genomes]
rs56151459	0.85[ASN][1000 genomes]
rs56193548	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56342397	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433395	0.90[CHB][hapmap];0.91[ASN][1000 genomes]
rs6741675	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67422536	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71417423	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72905046	0.90[ASN][1000 genomes]
rs72905080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12986917	ABCB11	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173943400-173974200	Weak transcription	Fetal Intestine Large	intestine
2	chr2:173945400-173991200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:173952000-173973400	Weak transcription	Hela-S3	cervix
4	chr2:173953800-173991400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:173955600-173984000	Weak transcription	Gastric	stomach
6	chr2:173955800-173977200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:173957000-173974400	Weak transcription	Fetal Stomach	stomach
8	chr2:173957800-173973400	Weak transcription	Fetal Lung	lung
9	chr2:173957800-173983800	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:173958000-173983800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:173958200-173973800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:173958200-173974000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:173959800-173974200	Weak transcription	HepG2	liver
14	chr2:173961400-173973400	Weak transcription	Fetal Intestine Small	intestine
15	chr2:173961800-173974400	Weak transcription	NHLF	lung
16	chr2:173962200-173983800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:173965000-173974000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:173965000-173987400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:173965400-173984400	Weak transcription	Aorta	Aorta
20	chr2:173965400-173987200	Weak transcription	Dnd41	blood
21	chr2:173965400-173989200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:173965600-173973800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr2:173965600-173983800	Weak transcription	Adipose Nuclei	Adipose
24	chr2:173966800-173973800	Weak transcription	NHEK	skin
25	chr2:173967200-173973200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:173967200-173973200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:173967600-173973800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:173968200-173974600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:173968600-173973600	Weak transcription	GM12878-XiMat	blood
30	chr2:173968600-173990600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:173969200-173987600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr2:173969400-173973400	Weak transcription	NH-A	brain
33	chr2:173970000-173973800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:173970000-173983200	Weak transcription	Right Atrium	heart
35	chr2:173971000-173974800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:173971200-173973200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr2:173971200-173973200	Enhancers	A549	lung
38	chr2:173971200-173973600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:173971200-173974000	Enhancers	Fetal Heart	heart
40	chr2:173971600-173973400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:173971600-173974800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:173971600-173985600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:173971800-173973200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:173971800-173973200	Weak transcription	HSMM	muscle
45	chr2:173971800-173973400	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:173971800-173973400	Weak transcription	HMEC	breast
47	chr2:173971800-173973600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:173971800-173980400	Weak transcription	Ovary	ovary
49	chr2:173972000-173973200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:173972000-173973600	Weak transcription	HSMMtube	muscle

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