Variant report

Variant	rs10880879
Chromosome Location	chr12:46367903-46367904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46354572..46357649-chr12:46367674..46371210,4	K562	blood:
2	chr12:46367766..46370474-chr12:46662022..46664572,2	K562	blood:
3	chr12:46365096..46367931-chr12:46383554..46385987,4	MCF-7	breast:
4	chr12:46365772..46368016-chr12:46375925..46378868,2	K562	blood:
5	chr12:46366328..46369312-chr12:46369671..46371966,2	K562	blood:

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction
ENSG00000139218	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1012642	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10748432	0.95[CEU][hapmap]
rs10785593	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880871	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880875	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880880	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];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880887	0.82[ASN][1000 genomes]
rs11183201	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11183210	0.80[JPT][hapmap]
rs11183241	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183243	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183268	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183272	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12314770	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs12826749	0.80[ASN][1000 genomes]
rs1366024	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1863127	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2059404	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs2408435	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs247917	0.82[ASN][1000 genomes]
rs247918	0.90[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs247919	0.85[ASN][1000 genomes]
rs247920	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs247929	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs247930	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs35115	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs35117	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs35121	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[ASN][1000 genomes]
rs35122	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs35125	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[ASN][1000 genomes]
rs6582574	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs7132422	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs724909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7298703	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308284	0.80[ASN][1000 genomes]
rs7311198	0.81[AMR][1000 genomes]
rs7315731	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[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	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[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];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[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	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
2	esv3439887	chr12:46337377-46370366	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 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	chr12:46329800-46371000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:46342200-46369000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:46343000-46375000	Weak transcription	NHEK	skin
5	chr12:46356400-46369200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:46356600-46374200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:46357000-46371000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:46357000-46380400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:46357200-46369000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:46357600-46380000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:46357800-46381200	Weak transcription	Fetal Kidney	kidney
12	chr12:46358800-46380600	Weak transcription	Spleen	Spleen
13	chr12:46360600-46369400	Weak transcription	Stomach Mucosa	stomach
14	chr12:46360600-46370400	Weak transcription	Brain Substantia Nigra	brain
15	chr12:46360600-46380000	Weak transcription	Brain Angular Gyrus	brain
16	chr12:46360600-46381400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:46360600-46381800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:46360600-46383000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:46360800-46370800	Weak transcription	Brain Anterior Caudate	brain
20	chr12:46361400-46383200	Weak transcription	Lung	lung
21	chr12:46361800-46368400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:46361800-46379600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:46362600-46368800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:46362800-46369000	Weak transcription	Right Atrium	heart
25	chr12:46362800-46369200	Weak transcription	Right Ventricle	heart
26	chr12:46362800-46383400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:46363200-46380200	Weak transcription	NHLF	lung
28	chr12:46363400-46368600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:46363400-46371800	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:46363400-46380600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:46363600-46371400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:46363600-46380600	Weak transcription	Fetal Stomach	stomach
33	chr12:46363600-46381800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:46363800-46372000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:46364000-46369200	Weak transcription	Pancreas	Pancrea
36	chr12:46364000-46370000	Strong transcription	Fetal Thymus	thymus
37	chr12:46364200-46368200	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr12:46364200-46370400	Strong transcription	Dnd41	blood
39	chr12:46364400-46368800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:46364400-46379000	Weak transcription	Gastric	stomach
41	chr12:46364800-46368600	Weak transcription	Liver	Liver
42	chr12:46365000-46369800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:46365000-46369800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:46365600-46372400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:46365600-46375400	Enhancers	Fetal Heart	heart
46	chr12:46366000-46372200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:46366200-46368000	Weak transcription	Psoas Muscle	Psoas
48	chr12:46366200-46368800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:46366200-46369400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:46366200-46370800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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