Variant report

Variant	rs6612632
Chromosome Location	chrX:56768856-56768857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chrX:56768375-56768918	U2OS	brain:	n/a	n/a
2	POLR2A	chrX:56768838-56768994	ProgFib	skin:	n/a	n/a

Variant related genes	Relation type
UQCRBP1	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12690340	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[TSI][hapmap]
rs1387716	0.83[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs1927222	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.85[MKK][hapmap]
rs2130431	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs5914709	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs5914710	0.82[CEU][hapmap];0.94[MEX][hapmap]
rs5914776	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.83[TSI][hapmap]
rs5914778	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap]
rs5914779	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5960204	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs5960738	0.83[ASW][hapmap];0.82[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]
rs5960754	0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap]
rs5960785	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs5960817	0.83[ASW][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752678	chrX:55930768-56851953	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2753382	chrX:55930768-56851953	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2754448	chrX:55930768-56851953	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2755974	chrX:55930768-56851953	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv432333	chrX:55930768-56851953	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2756104	chrX:56292362-56824154	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	esv2754937	chrX:56482424-56851953	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	esv2758569	chrX:56739069-56887748	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2758867	chrX:56739069-56887748	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv527262	chrX:56758231-56774826	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv510833	chrX:56766001-56841737	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6612632	SPIN-2	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:56756000-56780000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chrX:56757200-56769200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chrX:56757200-56773800	Weak transcription	HSMM	muscle
4	chrX:56757200-56775600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chrX:56757200-56777600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chrX:56757400-56771600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chrX:56757400-56779400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chrX:56757400-56788000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chrX:56757400-56791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chrX:56757400-56793200	Weak transcription	NH-A	brain
11	chrX:56757400-56793400	Weak transcription	Fetal Intestine Large	intestine
12	chrX:56757600-56779600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chrX:56757600-56800000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chrX:56757800-56788200	Weak transcription	Fetal Thymus	thymus
15	chrX:56758000-56773200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chrX:56758400-56771200	Weak transcription	HUVEC	blood vessel
17	chrX:56758400-56780400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chrX:56758400-56796200	Weak transcription	Brain Germinal Matrix	brain
19	chrX:56760800-56771400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chrX:56761600-56790400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chrX:56761800-56787600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chrX:56762000-56771200	Weak transcription	Hela-S3	cervix
23	chrX:56765200-56769600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chrX:56765200-56771200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chrX:56765200-56772400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chrX:56765200-56783000	Weak transcription	Primary B cells from peripheral blood	blood
27	chrX:56765400-56771200	Weak transcription	NHEK	skin
28	chrX:56765400-56773400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chrX:56765400-56773800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chrX:56765400-56815800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chrX:56765600-56783200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chrX:56765600-56783800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chrX:56765800-56773600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chrX:56766000-56777200	Weak transcription	Brain Hippocampus Middle	brain
35	chrX:56767000-56771400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chrX:56767800-56779400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chrX:56767800-56779400	Weak transcription	Dnd41	blood
38	chrX:56768000-56773800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chrX:56768200-56769600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chrX:56768400-56774000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chrX:56768600-56771200	Weak transcription	A549	lung
42	chrX:56768800-56783200	Weak transcription	Primary hematopoietic stem cells	blood

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