Variant report

Variant	rs6642857
Chromosome Location	chrX:110339676-110339677
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chrX:110339322-110339872	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF143	chrX:110339659-110339719	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chrX:110339024-110339825	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chrX:110339213-110339763	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chrX:110339041-110340243	H1-neurons	neurons:	n/a	n/a
6	REST	chrX:110338814-110340246	H1-neurons	neurons:	n/a	chrX:110339430-110339443
7	RAD21	chrX:110339490-110339801	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chrX:110338822-110340324	H1-hESC	embryonic stem cell:	n/a	chrX:110339430-110339443
9	POLR2A	chrX:110339321-110339743	IMR90	lung:	n/a	n/a
10	RFX5	chrX:110338671-110339890	SK-N-SH	brain:	n/a	chrX:110339337-110339346
11	POLR2A	chrX:110339001-110340123	H1-neurons	neurons:	n/a	n/a
12	CTCF	chrX:110339540-110339690	SK-N-SH_RA	brain:	n/a	n/a
13	RAD21	chrX:110339398-110339694	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrX:110339654-110339704	SK-N-SH_RA	brain:	n/a
2	chrX:110339654-110339704	HRPEpiC	eye:	n/a
3	chrX:110339654-110339704	NT2-D1	testis:	n/a
4	chrX:110339654-110339704	GM06990	blood:	n/a
5	chrX:110339654-110339704	HCPEpiC	choroid plexus:	n/a
6	chrX:110339654-110339704	Hepatocyte	liver:	n/a
7	chrX:110339654-110339704	HCT-116	colon:	n/a
8	chrX:110339654-110339704	AG04450	lung:	fetal
9	chrX:110339654-110339704	MCF10A-Er-Src	breast:	n/a
10	chrX:110339654-110339704	HEK293	kidney:	embryo
11	chrX:110339654-110339704	AG10803	skin:	n/a
12	chrX:110339654-110339704	GM12878	blood:	n/a
13	chrX:110339654-110339704	HepG2	liver:	n/a
14	chrX:110339654-110339704	NHDF-neo	bronchial:	n/a
15	chrX:110339654-110339704	K562	blood:	n/a
16	chrX:110339654-110339704	HMEC	breast:	n/a
17	chrX:110339654-110339704	AG04449	skin:	fetal
18	chrX:110339654-110339704	PANC-1	pancreas:	n/a
19	chrX:110339654-110339704	LNCaP	prostate:	n/a
20	chrX:110339654-110339704	HNPCEpiC	eye:	n/a
21	chrX:110339654-110339704	A549	lung:	n/a
22	chrX:110339654-110339704	SK-N-MC	brain:	n/a
23	chrX:110339654-110339704	AG09319	gingival:	n/a
24	chrX:110339654-110339704	NHBE	bronchial:	n/a
25	chrX:110339654-110339704	Jurkat	blood:	n/a
26	chrX:110339654-110339704	GM19239	blood:	n/a
27	chrX:110339654-110339704	HCM	heart:	n/a
28	chrX:110339654-110339704	HUVEC	blood vessel:	n/a
29	chrX:110339654-110339704	HAEpiC	amniotic membrane:	n/a
30	chrX:110339654-110339704	T-47D	breast:	n/a
31	chrX:110339654-110339704	H1-hESC	embryonic stem cell:	embryo
32	chrX:110339654-110339704	AG09309	skin:	n/a
33	chrX:110339654-110339704	GM12892	blood:	n/a
34	chrX:110339654-110339704	HIPEpiC	eye:	n/a
35	chrX:110339654-110339704	NH-A	brain:	n/a
36	chrX:110339654-110339704	HCF	heart:	n/a
37	chrX:110339654-110339704	HL-60	blood:	n/a
38	chrX:110339654-110339704	NB4	blood:	n/a
39	chrX:110339654-110339704	HEEpiC	esophagus:	n/a
40	chrX:110339654-110339704	AoSMC	blood vessel:	n/a
41	chrX:110339654-110339704	HRE	kidney:	n/a
42	chrX:110339654-110339704	RPTEC	kidney:	n/a
43	chrX:110339654-110339704	SKMC	muscle:	n/a
44	chrX:110339654-110339704	Hela-S3	cervix:	n/a
45	chrX:110339654-110339704	MCF-7	breast:	n/a
46	chrX:110339654-110339704	PFSK-1	brain:	n/a
47	chrX:110339654-110339704	CMK	blood:	n/a
48	chrX:110339654-110339704	SK-N-SH	brain:	n/a
49	chrX:110339654-110339704	U87	brain:	n/a
50	chrX:110339654-110339704	BJ	skin:	n/a

No data

Variant related genes	Relation type
PAK3	TF binding region
PAK3	CpG island

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10521531	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs1159650	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs12116264	1.00[CEU][hapmap]
rs1339302	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1339303	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1339304	1.00[CEU][hapmap]
rs1361320	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs16986368	1.00[CEU][hapmap]
rs16986378	1.00[CEU][hapmap]
rs16986384	1.00[CEU][hapmap]
rs16986385	1.00[CEU][hapmap]
rs1884552	1.00[CEU][hapmap]
rs1884554	1.00[CEU][hapmap]
rs1884555	1.00[CEU][hapmap]
rs2050750	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2050751	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap]
rs2066102	1.00[CEU][hapmap]
rs2208017	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs2208018	1.00[CEU][hapmap]
rs2208020	1.00[CEU][hapmap]
rs4341302	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4384152	0.84[ASW][hapmap];1.00[CEU][hapmap]
rs4514174	1.00[CEU][hapmap]
rs5942719	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs5942720	1.00[CEU][hapmap]
rs5942721	1.00[CEU][hapmap]
rs5943130	1.00[CEU][hapmap]
rs5943132	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs5943137	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs5985318	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap]
rs5985586	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs5985587	1.00[CEU][hapmap]
rs5985588	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap]
rs5985590	1.00[CEU][hapmap]
rs6642860	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6642862	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6642870	1.00[CEU][hapmap]
rs7879757	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs7881798	1.00[CEU][hapmap]
rs994591	1.00[CEU][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	nsv532899	chrX:110117241-110419226	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv428712	chrX:110184832-110358638	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv3337751	chrX:110217889-110429181	Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv869661	chrX:110337762-111084262	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:110338400-110339800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chrX:110338400-110342800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chrX:110338600-110339800	Active TSS	Brain Cingulate Gyrus	brain
4	chrX:110338600-110339800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
5	chrX:110338600-110340000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chrX:110338600-110340000	Active TSS	Aorta	Aorta
7	chrX:110338600-110340000	Active TSS	Brain Angular Gyrus	brain
8	chrX:110338600-110340000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chrX:110338600-110340200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chrX:110338600-110340200	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
11	chrX:110338600-110340200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
12	chrX:110338600-110340200	Bivalent/Poised TSS	Fetal Stomach	stomach
13	chrX:110338600-110340400	Active TSS	H1 Cell Line	embryonic stem cell
14	chrX:110338600-110340400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chrX:110338600-110340400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
16	chrX:110338600-110340400	Active TSS	HMEC	breast
17	chrX:110338600-110340400	Active TSS	NHLF	lung
18	chrX:110338600-110340600	Active TSS	Ovary	ovary
19	chrX:110338600-110340800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
20	chrX:110338600-110341800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chrX:110338800-110339800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chrX:110338800-110339800	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chrX:110338800-110339800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chrX:110338800-110339800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
25	chrX:110338800-110339800	Active TSS	Brain Hippocampus Middle	brain
26	chrX:110338800-110339800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
27	chrX:110338800-110339800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
28	chrX:110338800-110339800	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
29	chrX:110338800-110340000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chrX:110338800-110340000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chrX:110338800-110340000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chrX:110338800-110340000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chrX:110338800-110340000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chrX:110338800-110340000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
35	chrX:110338800-110340000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chrX:110338800-110340000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chrX:110338800-110340000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chrX:110338800-110340000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chrX:110338800-110340000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chrX:110338800-110340000	Active TSS	Duodenum Mucosa	Duodenum
41	chrX:110338800-110340000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
42	chrX:110338800-110340000	Bivalent/Poised TSS	Psoas Muscle	Psoas
43	chrX:110338800-110340000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
44	chrX:110338800-110340000	Active TSS	Right Atrium	heart
45	chrX:110338800-110340000	Active TSS	Right Ventricle	heart
46	chrX:110338800-110340200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chrX:110338800-110340400	Active TSS	H9 Cell Line	embryonic stem cell
48	chrX:110338800-110340400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chrX:110338800-110340400	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chrX:110338800-110340400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell

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