Variant report

Variant	rs2300197
Chromosome Location	chr6:134288661-134288662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:134276287..134278466-chr6:134288025..134290579,2	MCF-7	breast:
2	chr6:134271776..134274433-chr6:134288176..134289827,2	K562	blood:
3	chr6:134258577..134261545-chr6:134287191..134289671,3	K562	blood:
4	chr6:134280961..134282692-chr6:134285960..134288759,2	MCF-7	breast:
5	chr6:134273384..134275623-chr6:134288051..134290923,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000028839	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11154754	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1385066	0.81[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs162191	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162192	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs167876	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2076583	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs228867	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs35776966	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756877	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3777892	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs380825	0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs459625	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896019	0.84[CHD][hapmap]
rs6919121	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs9321424	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375994	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9385674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9389124	0.95[CHD][hapmap];0.84[AMR][1000 genomes]
rs9402553	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34122	chr6:134089019-134378252	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134275400-134289200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:134276200-134299000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:134276200-134303000	Weak transcription	HSMMtube	muscle
4	chr6:134276400-134290800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:134276400-134291000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:134276600-134288800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:134276600-134288800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:134276600-134288800	Weak transcription	HSMM	muscle
9	chr6:134276600-134293000	Weak transcription	Fetal Lung	lung
10	chr6:134276600-134302800	Weak transcription	Fetal Kidney	kidney
11	chr6:134276600-134314000	Weak transcription	Thymus	Thymus
12	chr6:134278000-134303600	Weak transcription	Dnd41	blood
13	chr6:134279400-134298800	Weak transcription	Psoas Muscle	Psoas
14	chr6:134279800-134294200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:134280400-134304200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:134280600-134293000	Weak transcription	Liver	Liver
17	chr6:134280600-134312200	Weak transcription	Lung	lung
18	chr6:134281000-134294400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:134281400-134288800	Weak transcription	A549	lung
20	chr6:134281400-134289800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:134281400-134298800	Weak transcription	Ovary	ovary
22	chr6:134282000-134298800	Weak transcription	Gastric	stomach
23	chr6:134282400-134289200	Genic enhancers	K562	blood
24	chr6:134282600-134302000	Weak transcription	Placenta	Placenta
25	chr6:134283000-134291000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr6:134283000-134294200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:134283200-134289800	Weak transcription	Right Atrium	heart
28	chr6:134283200-134305600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:134283400-134288800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:134283400-134289800	Weak transcription	Spleen	Spleen
31	chr6:134283400-134290800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:134283400-134293600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:134283600-134290400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:134283600-134290800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:134283600-134290800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:134283600-134290800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:134284000-134290800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:134285000-134316600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:134285800-134288800	Enhancers	Primary B cells from cord blood	blood
40	chr6:134285800-134288800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:134285800-134289000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr6:134285800-134289000	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr6:134286000-134288800	Enhancers	Primary B cells from peripheral blood	blood
44	chr6:134286000-134289000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:134286400-134288800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:134286400-134288800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:134286800-134288800	Enhancers	Brain Cingulate Gyrus	brain
48	chr6:134286800-134292400	Weak transcription	Fetal Brain Male	brain
49	chr6:134286800-134293800	Weak transcription	Fetal Brain Female	brain
50	chr6:134286800-134299000	Weak transcription	Monocytes-CD14+_RO01746	blood

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