Variant report

Variant	rs10880880
Chromosome Location	chr12:46375306-46375307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46348389..46350985-chr12:46373470..46376418,2	K562	blood:
2	chr12:46370168..46377627-chr12:46379598..46386227,22	MCF-7	breast:
3	chr12:46361324..46363006-chr12:46372617..46375436,2	MCF-7	breast:
4	chr12:46369343..46373226-chr12:46374858..46377675,3	K562	blood:
5	chr12:46368053..46370956-chr12:46373061..46376584,4	K562	blood:

Variant related genes	Relation type
ENSG00000139218	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1012642	0.80[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10748432	0.95[CEU][hapmap]
rs10748438	0.82[YRI][hapmap]
rs10785593	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880875	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880879	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880887	0.82[ASN][1000 genomes]
rs11183210	0.80[JPT][hapmap]
rs11183241	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183268	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11574952	0.85[YRI][hapmap]
rs12314770	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap]
rs12826749	0.80[ASN][1000 genomes]
rs1366024	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17096380	1.00[LWK][hapmap];0.85[YRI][hapmap]
rs1863127	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs2059404	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs2408435	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs247917	0.82[ASN][1000 genomes]
rs247918	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs247919	0.85[ASN][1000 genomes]
rs247920	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs247929	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs247930	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap]
rs35115	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs35117	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap]
rs35121	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs35122	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs35125	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs6582574	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs7132422	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs724909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7298703	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308284	0.80[ASN][1000 genomes]
rs7311198	0.85[AMR][1000 genomes]
rs7315731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7966125	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7967208	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7970129	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7976870	0.96[CEU][hapmap];0.81[ASN][1000 genomes]
rs997307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[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	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:46357000-46380400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:46357600-46380000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:46357800-46381200	Weak transcription	Fetal Kidney	kidney
5	chr12:46358800-46380600	Weak transcription	Spleen	Spleen
6	chr12:46360600-46380000	Weak transcription	Brain Angular Gyrus	brain
7	chr12:46360600-46381400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:46360600-46381800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:46360600-46383000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:46361400-46383200	Weak transcription	Lung	lung
11	chr12:46361800-46379600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:46362800-46383400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:46363200-46380200	Weak transcription	NHLF	lung
14	chr12:46363400-46380600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:46363600-46380600	Weak transcription	Fetal Stomach	stomach
16	chr12:46363600-46381800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:46364400-46379000	Weak transcription	Gastric	stomach
18	chr12:46365600-46375400	Enhancers	Fetal Heart	heart
19	chr12:46366200-46377800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr12:46366200-46378400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:46366400-46377800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:46366400-46379000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:46366400-46380200	Weak transcription	Thymus	Thymus
24	chr12:46366400-46380600	Weak transcription	Placenta	Placenta
25	chr12:46367400-46379000	Weak transcription	Fetal Intestine Large	intestine
26	chr12:46367400-46383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:46367600-46376600	Weak transcription	Hela-S3	cervix
28	chr12:46367800-46380400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:46368200-46379200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:46368600-46380600	Weak transcription	NH-A	brain
31	chr12:46368800-46380600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:46369000-46379200	Weak transcription	NHDF-Ad	bronchial
33	chr12:46369200-46378200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:46369200-46379200	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:46369200-46380600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:46369400-46379200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:46369600-46375400	Weak transcription	Left Ventricle	heart
38	chr12:46369600-46376200	Weak transcription	Right Atrium	heart
39	chr12:46369600-46378200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:46369600-46380400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:46369600-46380400	Weak transcription	Pancreas	Pancrea
42	chr12:46369800-46379000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:46370000-46375400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:46370000-46375400	Weak transcription	Fetal Intestine Small	intestine
45	chr12:46370000-46377800	Weak transcription	Fetal Thymus	thymus
46	chr12:46370000-46379800	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:46370000-46381000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:46370200-46377200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:46370200-46378000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:46370400-46376600	Weak transcription	Dnd41	blood

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