Variant report

Variant	rs6463554
Chromosome Location	chr7:6437801-6437802
allele	C/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	chr7:6437760-6438195	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:6437783-6438070	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6412448..6415033-chr7:6435116..6438429,3	MCF-7	breast:
2	chr7:6413015..6417903-chr7:6435938..6439469,5	MCF-7	breast:

Variant related genes	Relation type
RAC1	TF binding region
ENSG00000136238	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10499343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10499344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1075434	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34178055	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34183253	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34215517	0.80[AMR][1000 genomes]
rs34609290	0.92[ASN][1000 genomes]
rs34762204	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35057107	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35326930	0.92[ASN][1000 genomes]
rs35530051	1.00[ASN][1000 genomes]
rs35589149	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35649698	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35699473	0.92[ASN][1000 genomes]
rs35887529	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3729793	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3813518	0.85[AFR][1000 genomes]
rs4397303	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56228579	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6463552	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6463553	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6942723	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73341292	0.84[AFR][1000 genomes]
rs73342949	0.84[AFR][1000 genomes]
rs768409	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7784465	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7790101	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792815	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs866279	0.81[MEX][hapmap];0.87[TSI][hapmap]
rs929926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer 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	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv605999	chr7:6396719-6472881	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	esv1824738	chr7:6431933-6554222	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	esv1825865	chr7:6431933-6554222	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6426000-6456400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:6426000-6475600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:6426400-6457400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:6432800-6438600	Enhancers	Left Ventricle	heart
5	chr7:6433200-6441200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:6433600-6441200	Weak transcription	Fetal Kidney	kidney
7	chr7:6433800-6440600	Weak transcription	HSMMtube	muscle
8	chr7:6434000-6438000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:6434000-6438600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:6434000-6439600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:6434000-6439600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:6434200-6438000	Weak transcription	NH-A	brain
13	chr7:6434200-6438600	Weak transcription	Fetal Lung	lung
14	chr7:6434200-6441200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:6434200-6441200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr7:6434400-6438600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:6434400-6439200	Weak transcription	NHDF-Ad	bronchial
18	chr7:6434400-6439600	Weak transcription	Aorta	Aorta
19	chr7:6434400-6440800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:6434600-6438800	Weak transcription	Primary T cells from cord blood	blood
21	chr7:6435600-6439600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:6435800-6438000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr7:6435800-6438200	Weak transcription	Colonic Mucosa	Colon
24	chr7:6435800-6439200	Enhancers	Brain Hippocampus Middle	brain
25	chr7:6436000-6438000	Strong transcription	Fetal Intestine Small	intestine
26	chr7:6436000-6440200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:6436000-6440800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:6436000-6444800	Weak transcription	Fetal Brain Male	brain
29	chr7:6436200-6438000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:6436200-6438000	Weak transcription	Gastric	stomach
31	chr7:6436200-6438000	Weak transcription	Osteobl	bone
32	chr7:6436200-6438400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:6436200-6438600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:6436200-6438600	Weak transcription	NHLF	lung
35	chr7:6436200-6439200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:6436200-6439600	Weak transcription	HUVEC	blood vessel
37	chr7:6436200-6440800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr7:6436200-6441000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr7:6436200-6441200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr7:6436200-6448200	Weak transcription	Small Intestine	intestine
41	chr7:6436400-6438000	Weak transcription	Colon Smooth Muscle	Colon
42	chr7:6436400-6438200	Weak transcription	Primary B cells from cord blood	blood
43	chr7:6436400-6438200	Weak transcription	Hela-S3	cervix
44	chr7:6436400-6438600	Weak transcription	Liver	Liver
45	chr7:6436400-6439600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr7:6437000-6438600	Enhancers	Brain Cingulate Gyrus	brain
47	chr7:6437000-6438600	Enhancers	Right Atrium	heart
48	chr7:6437000-6438800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:6437000-6439600	Enhancers	Psoas Muscle	Psoas
50	chr7:6437200-6438400	Enhancers	Stomach Smooth Muscle	stomach

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