Variant report

Variant	rs12619629
Chromosome Location	chr2:38776117-38776118
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38741728..38744582-chr2:38773775..38776381,2	K562	blood:
2	chr2:38772538..38776626-chr2:38827465..38831623,3	K562	blood:
3	chr2:38773369..38778839-chr2:38780028..38785171,8	K562	blood:
4	chr2:38771801..38777092-chr2:38966712..38971904,5	K562	blood:

Variant related genes	Relation type
ENSG00000235586	Chromatin interaction
ENSG00000231367	Chromatin interaction
ENSG00000143889	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12614876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12616367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12621565	0.88[ASN][1000 genomes]
rs12621788	0.83[EUR][1000 genomes]
rs1543881	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17576044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs17603782	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs34133986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36024292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731842	1.00[AFR][1000 genomes]
rs3765001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55785223	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55833813	0.83[EUR][1000 genomes]
rs56956410	0.83[EUR][1000 genomes]
rs6544165	1.00[CEU][hapmap]
rs6754893	0.83[EUR][1000 genomes]
rs6760965	1.00[CEU][hapmap]
rs72895897	0.83[EUR][1000 genomes]
rs72905831	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72905839	0.83[EUR][1000 genomes]
rs73929040	0.83[EUR][1000 genomes]
rs73929052	0.83[EUR][1000 genomes]
rs7578356	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7579783	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7584862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7606515	1.00[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv1796304	chr2:38766721-38790750	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38763800-38778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
4	chr2:38768400-38787800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:38768400-38788000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:38768800-38779000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:38769000-38793200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:38769200-38776800	Weak transcription	Brain Anterior Caudate	brain
10	chr2:38769200-38782800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:38769200-38787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:38769200-38788400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:38769600-38777000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:38770000-38788600	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:38770200-38777600	Weak transcription	HSMM	muscle
16	chr2:38770200-38781000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:38770400-38776200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:38770400-38776200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:38770400-38776400	Weak transcription	Ovary	ovary
20	chr2:38770400-38778400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:38770400-38778800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:38770400-38778800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:38770400-38778800	Weak transcription	HSMMtube	muscle
24	chr2:38770400-38786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:38770400-38787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:38770400-38787200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:38770400-38787200	Weak transcription	Fetal Intestine Large	intestine
28	chr2:38770400-38787200	Weak transcription	NHLF	lung
29	chr2:38770400-38787200	Weak transcription	Osteobl	bone
30	chr2:38770400-38787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:38770400-38787400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:38770400-38791000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:38770400-38794600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:38770600-38785800	Weak transcription	NH-A	brain
35	chr2:38770600-38787400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:38770600-38794800	Weak transcription	NHEK	skin
37	chr2:38770800-38794400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:38771000-38779400	Weak transcription	Fetal Thymus	thymus
39	chr2:38771000-38786200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:38771200-38776200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:38771200-38776200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:38771200-38776200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:38771200-38776400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:38771200-38778800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:38771200-38781000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:38771200-38787200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:38771200-38787400	Weak transcription	HUVEC	blood vessel
48	chr2:38771400-38776400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:38771400-38776400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:38772000-38776200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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