Variant report

Variant	rs9429888
Chromosome Location	chr1:212789399-212789400
allele	A/G
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	POLR2A	chr1:212787958-212789681	K562	blood:	n/a	n/a
2	POLR2A	chr1:212788956-212789509	K562	blood:	n/a	n/a
3	POLR2A	chr1:212787946-212789828	Hela-S3	cervix:	n/a	n/a
4	USF2	chr1:212789397-212789438	Hela-S3	cervix:	n/a	chr1:212789397-212789408
5	POLR2A	chr1:212789327-212789655	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:212781346-212789662	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:212780144-212798001	IMR90	lung:	n/a	n/a
8	POLR2A	chr1:212788347-212789461	K562	blood:	n/a	n/a
9	POLR2A	chr1:212787968-212791124	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:212788955-212789534	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:212788106-212789627	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:212788300-212789505	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:212782514-212798502	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212780858..212783878-chr1:212789179..212792370,4	MCF-7	breast:
2	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
3	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:

Variant related genes	Relation type
RN7SL512P	TF binding region
ENSG00000162772	Chromatin interaction
ENSG00000260805	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11119988	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs1126526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739715	1.00[CHB][hapmap]
rs17019266	1.00[CHB][hapmap]
rs17019397	1.00[CHB][hapmap]
rs17019510	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2007776	1.00[CHB][hapmap]
rs2359321	1.00[CHB][hapmap]
rs2456815	1.00[CHB][hapmap]
rs492231	1.00[CHB][hapmap]
rs4951627	0.86[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs536040	1.00[CHB][hapmap]
rs641053	1.00[CHB][hapmap]
rs7549085	1.00[CHB][hapmap]

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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212783400-212790400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:212783400-212791600	Weak transcription	Ovary	ovary
3	chr1:212783600-212792000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:212784000-212792000	Weak transcription	Esophagus	oesophagus
5	chr1:212784000-212794200	Weak transcription	HUVEC	blood vessel
6	chr1:212784200-212790400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:212784200-212796800	Weak transcription	Stomach Mucosa	stomach
8	chr1:212784400-212790200	Weak transcription	Dnd41	blood
9	chr1:212784400-212790400	Weak transcription	Colonic Mucosa	Colon
10	chr1:212784800-212790400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:212784800-212794800	Weak transcription	NH-A	brain
12	chr1:212785000-212790200	Weak transcription	Psoas Muscle	Psoas
13	chr1:212785000-212797000	Weak transcription	Right Atrium	heart
14	chr1:212785000-212801000	Weak transcription	Fetal Heart	heart
15	chr1:212785400-212790000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:212785400-212795600	Weak transcription	A549	lung
17	chr1:212785800-212792400	Weak transcription	Small Intestine	intestine
18	chr1:212786400-212794000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:212786600-212790200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:212786600-212795200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:212786800-212791600	Weak transcription	Fetal Lung	lung
22	chr1:212787000-212794000	Strong transcription	Fetal Intestine Small	intestine
23	chr1:212787000-212794400	Strong transcription	Stomach Smooth Muscle	stomach
24	chr1:212787200-212791600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:212787600-212790000	Weak transcription	Spleen	Spleen
26	chr1:212787600-212792400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:212787600-212793800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:212787600-212793800	Strong transcription	Right Ventricle	heart
29	chr1:212787600-212793800	Strong transcription	K562	blood
30	chr1:212787600-212794400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:212787600-212794400	Strong transcription	NHLF	lung
32	chr1:212787600-212795000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:212787800-212791600	Weak transcription	NHDF-Ad	bronchial
34	chr1:212788000-212794200	Strong transcription	Fetal Stomach	stomach
35	chr1:212788200-212789600	Strong transcription	Primary hematopoietic stem cells	blood
36	chr1:212788200-212792400	Strong transcription	Lung	lung
37	chr1:212788200-212793600	Strong transcription	HepG2	liver
38	chr1:212788200-212794200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:212788200-212794400	Strong transcription	Adipose Nuclei	Adipose
40	chr1:212788200-212794400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:212788200-212794600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:212788200-212794600	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:212788200-212794800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:212788200-212795000	Strong transcription	Liver	Liver
45	chr1:212788200-212795200	Strong transcription	Placenta	Placenta
46	chr1:212788400-212789600	Strong transcription	Colon Smooth Muscle	Colon
47	chr1:212788400-212789800	Strong transcription	Brain Substantia Nigra	brain
48	chr1:212788400-212791600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:212788400-212792000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:212788400-212792200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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