Variant report

Variant	rs12139863
Chromosome Location	chr1:70634585-70634586
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70634010..70636931-chr1:70644146..70645771,2	K562	blood:
2	chr1:70632648..70635188-chr1:70637548..70640122,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10518334	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12136628	0.86[JPT][hapmap]
rs12565719	0.92[CEU][hapmap]
rs12725762	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs12737233	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12741805	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs12748551	0.87[GIH][hapmap]
rs17506335	1.00[ASW][hapmap]
rs34495920	0.85[CEU][hapmap]
rs34766759	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531879	chr1:70386455-70644617	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005397	chr1:70598803-70634585	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12139863	HHLA3	cis	parietal	SCAN
rs12139863	LRRC7	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70601000-70643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:70601200-70652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:70603400-70648800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:70605400-70639400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:70606800-70634800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:70606800-70634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:70606800-70651600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:70606800-70661800	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:70607000-70670200	Weak transcription	Psoas Muscle	Psoas
10	chr1:70607000-70670400	Weak transcription	Small Intestine	intestine
11	chr1:70607200-70652600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:70607400-70655200	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:70608200-70645400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:70608400-70653400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:70608800-70654800	Weak transcription	Thymus	Thymus
16	chr1:70608800-70655800	Weak transcription	Esophagus	oesophagus
17	chr1:70609200-70647600	Weak transcription	Colonic Mucosa	Colon
18	chr1:70609200-70650200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:70609400-70638800	Weak transcription	Placenta	Placenta
20	chr1:70609400-70649800	Weak transcription	Fetal Brain Male	brain
21	chr1:70609600-70661200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:70610000-70642600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:70610000-70656600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:70610000-70667800	Weak transcription	HepG2	liver
25	chr1:70610400-70650200	Weak transcription	GM12878-XiMat	blood
26	chr1:70610400-70653600	Weak transcription	Gastric	stomach
27	chr1:70610600-70669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:70611000-70666600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:70611200-70645000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:70611200-70670400	Weak transcription	Pancreas	Pancrea
31	chr1:70611400-70652800	Weak transcription	Spleen	Spleen
32	chr1:70611600-70643000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:70612400-70669000	Weak transcription	HUVEC	blood vessel
34	chr1:70613000-70649200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:70613400-70638000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:70613400-70658400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:70613600-70657000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:70613600-70667800	Weak transcription	Brain Angular Gyrus	brain
39	chr1:70613800-70643000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:70613800-70645200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:70613800-70649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:70613800-70658000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:70614400-70651000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:70614400-70657800	Weak transcription	Fetal Kidney	kidney
45	chr1:70615000-70670000	Weak transcription	NH-A	brain
46	chr1:70615000-70670400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:70615200-70637200	Weak transcription	HSMM	muscle
48	chr1:70615200-70643000	Weak transcription	Ovary	ovary
49	chr1:70615200-70649200	Weak transcription	Left Ventricle	heart
50	chr1:70616400-70649200	Weak transcription	Fetal Lung	lung

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