Variant report

Variant	rs10165399
Chromosome Location	chr2:191441595-191441596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191398265..191400874-chr2:191441463..191447520,6	MCF-7	breast:
2	chr2:191435113..191437081-chr2:191440439..191443139,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233654	Chromatin interaction
ENSG00000189362	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10173771	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11680758	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12611871	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13006708	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410230	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452331	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321393	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853513	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4853719	0.80[AFR][1000 genomes]
rs6434402	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724607	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741118	0.80[AFR][1000 genomes]
rs7598979	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7603849	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630991	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9967829	0.83[YRI][hapmap]

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	nsv834492	chr2:191438864-191646621	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10165399	HIBCH	cis	lymphoblastoid	seeQTL
rs10165399	HIBCH	cis	Muscle Skeletal	GTEx
rs10165399	INPP1	cis	cerebellum	SCAN
rs10165399	MFSD6	cis	cerebellum	SCAN
rs10165399	TMEM194B	cis	cerebellum	SCAN
rs10165399	HIBCH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191411000-191443000	Weak transcription	Right Atrium	heart
2	chr2:191427200-191443000	Weak transcription	Right Ventricle	heart
3	chr2:191435400-191443000	Weak transcription	Left Ventricle	heart
4	chr2:191436800-191442800	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:191436800-191443000	Weak transcription	Brain Anterior Caudate	brain
6	chr2:191436800-191457000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:191437400-191442800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:191438400-191442600	Weak transcription	Stomach Mucosa	stomach
9	chr2:191438400-191442800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:191438400-191442800	Weak transcription	Fetal Intestine Small	intestine
11	chr2:191438400-191442800	Weak transcription	Fetal Lung	lung
12	chr2:191438400-191442800	Weak transcription	Small Intestine	intestine
13	chr2:191439200-191442600	Weak transcription	Fetal Stomach	stomach
14	chr2:191439400-191442600	Weak transcription	HMEC	breast
15	chr2:191439400-191442800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:191439800-191442800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:191439800-191443000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:191440200-191442800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:191440600-191442800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:191440600-191443000	Weak transcription	Fetal Thymus	thymus
21	chr2:191440600-191443400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:191440800-191441600	Active TSS	Stomach Smooth Muscle	stomach
23	chr2:191440800-191441800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:191440800-191442600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:191440800-191443000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:191440800-191445200	Enhancers	Fetal Heart	heart
27	chr2:191441000-191441800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:191441000-191441800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:191441000-191441800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr2:191441000-191442000	Flanking Active TSS	NHEK	skin
31	chr2:191441000-191442200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr2:191441000-191442600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:191441000-191442800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:191441000-191442800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:191441000-191442800	Enhancers	A549	lung
36	chr2:191441200-191441800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr2:191441200-191442200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:191441200-191442800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:191441200-191443000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:191441400-191441600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:191441400-191441600	Enhancers	Duodenum Mucosa	Duodenum
42	chr2:191441400-191441600	Enhancers	Spleen	Spleen
43	chr2:191441400-191441800	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr2:191441400-191442000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:191441400-191442000	Enhancers	Primary T cells from cord blood	blood
46	chr2:191441400-191442000	Enhancers	K562	blood
47	chr2:191441400-191442800	Enhancers	Hela-S3	cervix
48	chr2:191441400-191443000	Enhancers	Colon Smooth Muscle	Colon
49	chr2:191441400-191443400	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr2:191441400-191443600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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