Variant report

Variant	rs6462949
Chromosome Location	chr7:39831736-39831737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:88)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:88 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr7:39831649-39831780	GM10248	blood:	n/a	n/a
2	CTCFL	chr7:39831611-39831754	K562	blood:	n/a	n/a
3	CTCF	chr7:39831620-39831770	HRE	kidney:	n/a	n/a
4	CTCF	chr7:39831660-39831810	A549	lung:	n/a	n/a
5	CTCF	chr7:39831620-39831770	GM12872	blood:	n/a	n/a
6	RAD21	chr7:39831466-39831948	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCFL	chr7:39831635-39831756	K562	blood:	n/a	n/a
8	CTCF	chr7:39831583-39831828	K562	blood:	n/a	n/a
9	CTCF	chr7:39831605-39831783	GM19238	blood:	n/a	n/a
10	RAD21	chr7:39831646-39831741	K562	blood:	n/a	n/a
11	CTCF	chr7:39831579-39831815	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr7:39831627-39831789	GM12878	blood:	n/a	n/a
13	CTCF	chr7:39831640-39831790	GM12868	blood:	n/a	n/a
14	CTCF	chr7:39831600-39831750	K562	blood:	n/a	n/a
15	CBX3	chr7:39831433-39831839	K562	blood:	n/a	n/a
16	CTCF	chr7:39831600-39831750	HUVEC	blood vessel:	n/a	n/a
17	CTCF	chr7:39831600-39831750	HPAF	blood vessel:	n/a	n/a
18	RAD21	chr7:39831556-39831882	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr7:39831620-39831770	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr7:39831547-39831760	SK-N-SH_RA	brain:	n/a	n/a
21	CTCF	chr7:39831644-39831753	GM19239	blood:	n/a	n/a
22	CTCF	chr7:39831479-39831901	K562	blood:	n/a	n/a
23	CTCF	chr7:39831602-39831791	GM12891	blood:	n/a	n/a
24	CTCF	chr7:39831608-39831778	MCF-7	breast:	n/a	n/a
25	CTCF	chr7:39831620-39831770	BE2_C	brain:	n/a	n/a
26	CTCF	chr7:39831611-39831775	GM12892	blood:	n/a	n/a
27	CTCF	chr7:39831532-39831821	H1-hESC	embryonic stem cell:	n/a	n/a
28	SMC3	chr7:39831312-39832004	SK-N-SH	brain:	n/a	n/a
29	CTCF	chr7:39831668-39831787	GM20000	blood:	n/a	n/a
30	CTCF	chr7:39831660-39831810	GM12870	blood:	n/a	n/a
31	CTCF	chr7:39831640-39831790	HVMF	connective:	n/a	n/a
32	CTCF	chr7:39831620-39831770	HMEC	breast:	n/a	n/a
33	CTCF	chr7:39831620-39831770	SK-N-SH_RA	brain:	n/a	n/a
34	CTCF	chr7:39831363-39832014	SK-N-SH	brain:	n/a	n/a
35	CTCF	chr7:39831660-39831930	RPTEC	kidney:	n/a	n/a
36	CTCF	chr7:39831600-39831801	MCF-7	breast:	n/a	n/a
37	SMC3	chr7:39831681-39831767	K562	blood:	n/a	n/a
38	CTCF	chr7:39831599-39831792	SK-N-SH_RA	brain:	n/a	n/a
39	CTCF	chr7:39831717-39831759	IMR90	lung:	n/a	n/a
40	RAD21	chr7:39831463-39831892	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr7:39831600-39831750	GM12874	blood:	n/a	n/a
42	RAD21	chr7:39831491-39831795	SK-N-SH_RA	brain:	n/a	n/a
43	CTCF	chr7:39831620-39831770	HA-sp	spinal cord:	n/a	n/a
44	CTCF	chr7:39831666-39831751	LNCaP	prostate:	n/a	n/a
45	CTCF	chr7:39831583-39831812	MCF-7	breast:	n/a	n/a
46	CTCF	chr7:39831600-39831750	NHEK	skin:	n/a	n/a
47	RAD21	chr7:39831474-39831897	SK-N-SH_RA	brain:	n/a	n/a
48	CTCF	chr7:39831668-39831772	HepG2	liver:	n/a	n/a
49	CTCF	chr7:39831600-39831750	HRPEpiC	eye:	n/a	n/a
50	CTCF	chr7:39831590-39831779	GM13977	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39619917..39620450-chr7:39831240..39831746,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270797	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10231605	0.81[ASN][1000 genomes]
rs1964239	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34326443	0.83[ASN][1000 genomes]
rs3873649	0.81[ASN][1000 genomes]
rs4723903	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4723906	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6462948	0.81[ASN][1000 genomes]
rs71536648	0.81[ASN][1000 genomes]
rs71536651	0.81[ASN][1000 genomes]
rs73379510	0.81[ASN][1000 genomes]
rs9770188	0.82[AMR][1000 genomes]
rs9770412	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9770818	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv970820	chr7:39797964-39839303	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv5708	chr7:39814330-39855535	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv981627	chr7:39819869-39837441	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv887974	chr7:39827400-39956829	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39785000-39831800	Weak transcription	Primary B cells from cord blood	blood
2	chr7:39794200-39837400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:39795400-39833400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr7:39801600-39833600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:39802000-39835200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:39802600-39833000	Weak transcription	Dnd41	blood
7	chr7:39802800-39835000	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:39803400-39832000	Weak transcription	Fetal Thymus	thymus
9	chr7:39805200-39834400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:39807800-39832800	Weak transcription	Brain Anterior Caudate	brain
11	chr7:39808200-39833000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:39808200-39833800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr7:39808400-39832800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:39808400-39833200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr7:39810600-39837200	Weak transcription	Brain Substantia Nigra	brain
16	chr7:39811000-39835800	Weak transcription	Brain Germinal Matrix	brain
17	chr7:39812400-39837400	Weak transcription	Fetal Intestine Large	intestine
18	chr7:39812400-39837600	Weak transcription	Spleen	Spleen
19	chr7:39820600-39833000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:39821400-39839000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr7:39821600-39835600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:39822000-39834200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:39822000-39834600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:39822200-39835000	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:39822400-39832800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr7:39822800-39836200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:39825000-39834400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:39828400-39832200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr7:39828800-39836400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr7:39829000-39832000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:39829200-39832400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:39829200-39835000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr7:39829400-39834400	Weak transcription	Colonic Mucosa	Colon
34	chr7:39829600-39833400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:39830200-39832000	Strong transcription	Aorta	Aorta
36	chr7:39830200-39833600	Strong transcription	Fetal Stomach	stomach
37	chr7:39830400-39836600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr7:39830600-39831800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:39830800-39831800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr7:39830800-39831800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr7:39830800-39831800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:39830800-39831800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:39830800-39831800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr7:39830800-39831800	Strong transcription	Ovary	ovary
45	chr7:39830800-39832000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:39830800-39832000	Strong transcription	Pancreas	Pancrea
47	chr7:39830800-39832400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr7:39830800-39833600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:39830800-39833600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:39830800-39833600	Strong transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links